release

.bidsignore

@@ -1,3 +1,4 @@
 **/anat/*localizer*
 **/anat/*scout*
-**/*__dup*
+**/*_dup*
+**/gamelogs/*

.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

.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: [email protected]
+    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 }}

.gitmodules

@@ -0,0 +1,5 @@
+[submodule "stimuli"]
+	path = stimuli
+	url = [email protected]:courtois-neuromod/mario3.stimuli.git
+	datalad-id = caf26616-f8f9-41d8-b9b8-6471a4591395
+	datalad-url = https://github.com/courtois-neuromod/mario3.stimuli.git

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)

README

@@ -1,13 +1,13 @@
 <!-- vim: syntax=Markdown -->
-# 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)

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": "<xxxxx> sub-dataset of the Courtois-Neuromod project",
+    "Name": "mario3 sub-dataset of the Courtois-Neuromod project",
     "ReferencesAndLinks": [
         "https://docs.cneuromod.ca/"
     ]

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)"
+  }
+}

participants.tsv

@@ -0,0 +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

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"
+  }
+}

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
+}

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

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
+}

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

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
+}

sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/ZP/xQ/MD5E-s620846--6c305c91bcec10032ce0d84c0692f4e2.nii.gz/MD5E-s620846--6c305c91bcec10032ce0d84c0692f4e2.nii.gz