diff --git a/circle.yml b/circle.yml index bcb488b..86bafee 100644 --- a/circle.yml +++ b/circle.yml @@ -16,4 +16,3 @@ test: - docker-compose -f dockereve-master/docker-compose.yml up -d - sleep 60 - python test/testGetPost.py - \ No newline at end of file diff --git a/dockereve-master/eve-app/settings.py b/dockereve-master/eve-app/settings.py index 713f938..910ab16 100644 --- a/dockereve-master/eve-app/settings.py +++ b/dockereve-master/eve-app/settings.py @@ -1,8 +1,11 @@ import os import re +from copy import deepcopy + get_mongo_host = re.match('tcp://(.*):(.*)', os.environ['MONGODB_PORT']) bids_schema = { + # BIDS identification bits 'modality': { 'type': 'string', 'required': True @@ -15,9 +18,71 @@ 'acq_id': {'type': 'string'}, 'task_id': {'type': 'string'}, 'run_id': {'type': 'string'}, + # BIDS metadata + 'AccelNumReferenceLines': {'type': 'integer'}, + 'AccelerationFactorPE': {'type': 'integer'}, + 'AcquisitionMatrix': {'type': 'string'}, + 'CogAtlasID': {'type': 'string'}, + 'CogPOID': {'type': 'string'}, + 'CoilCombinationMethod': {'type': 'string'}, + 'ContrastBolusIngredient': {'type': 'string'}, + 'ConversionSoftware': {'type': 'string'}, + 'ConversionSoftwareVersion': {'type': 'string'}, + 'DelayTime': {'type': 'float'}, + 'DeviceSerialNumber': {'type': 'string'}, + 'EchoTime': {'type': 'float'}, + 'EchoTrainLength': {'type': 'integer'}, + 'EffectiveEchoSpacing': {'type': 'float'}, + 'FlipAngle': {'type': 'integer'}, + 'GradientSetType': {'type': 'string'}, + 'HardcopyDeviceSoftwareVersion': {'type': 'string'}, + 'ImageType': {'type': 'string'}, + 'ImagingFrequency': {'type': 'integer'}, + 'InPlanePhaseEncodingDirection': {'type': 'string'}, + 'InstitutionAddress': {'type': 'string'}, + 'InstitutionName': {'type': 'string'}, + 'Instructions': {'type': 'string'}, + 'InversionTime': {'type': 'float'}, + 'MRAcquisitionType': {'type': 'string'}, + 'MRTransmitCoilSequence': {'type': 'string'}, + 'MagneticFieldStrength': {'type': 'integer'}, + 'Manufacturer': {'type': 'string'}, + 'ManufacturersModelName': {'type': 'string'}, + 'MatrixCoilMode': {'type': 'string'}, + 'MultibandAccelerationFactor': {'type': 'float'}, + 'NumberOfAverages': {'type': 'integer'}, + 'NumberOfPhaseEncodingSteps': {'type': 'integer'}, + 'NumberOfVolumesDiscardedByScanner': {'type': 'float'}, + 'NumberOfVolumesDiscardedByUser': {'type': 'float'}, + 'NumberShots': {'type': 'integer'}, + 'ParallelAcquisitionTechnique': {'type': 'string'}, + 'ParallelReductionFactorInPlane': {'type': 'float'}, + 'PartialFourier': {'type': 'boolean'}, + 'PartialFourierDirection': {'type': 'string'}, + 'PatientPosition': {'type': 'string'}, + 'PercentPhaseFieldOfView': {'type': 'integer'}, + 'PercentSampling': {'type': 'integer'}, + 'PhaseEncodingDirection': {'type': 'string'}, + 'PixelBandwidth': {'type': 'integer'}, + 'ProtocolName': {'type': 'string'}, + 'PulseSequenceDetails': {'type': 'string'}, + 'PulseSequenceType': {'type': 'string'}, + 'ReceiveCoilName': {'type': 'string'}, + 'RepetitionTime': {'type': 'float'}, + 'ScanOptions': {'type': 'string'}, + 'ScanningSequence': {'type': 'string'}, + 'SequenceName': {'type': 'string'}, + 'SequenceVariant': {'type': 'string'}, + 'SliceEncodingDirection': {'type': 'string'}, + 'SoftwareVersions': {'type': 'string'}, + 'TaskDescription': {'type': 'string'}, + 'TotalReadoutTime': {'type': 'float'}, + 'TotalScanTimeSec': {'type': 'integer'}, + 'TransmitCoilName': {'type': 'string'}, + 'VariableFlipAngleFlag': {'type': 'string'}, } -settings_schema = { +prov_schema = { 'version': { 'type': 'string', 'required': True @@ -30,6 +95,15 @@ 'type': 'string', 'required': True }, + 'settings': { + 'type': 'dict', + 'schema': { + 'fd_thres': {'type': 'float'}, + 'hmc_fsl': {'type': 'boolean'}, + 'testing': {'type': 'boolean'} + }, + }, + 'mriqc_pred': {'type': 'integer'}, } bold_iqms_schema = { @@ -42,6 +116,7 @@ 'required': True }, + 'dummy_trs': {'type': 'integer'}, 'dvars_nstd': { 'type': 'float', 'required': True @@ -264,10 +339,6 @@ 'type': 'float', 'required': True }, - 'mriqc_pred': { - 'type': 'integer', - 'required': True - }, 'qi_1': { 'type': 'float', 'required': True @@ -489,153 +560,53 @@ 'item_title': 'bold', 'resource_methods': ['GET', 'POST'], 'item_methods': ['GET', 'PATCH', 'PUT', 'DELETE'], - 'schema': { - # if modality == bold, the fields below are required - 'TaskName': { - 'type': 'string', - 'required': True - }, - 'AccelNumReferenceLines': {'type': 'integer'}, - 'AccelerationFactorPE': {'type': 'integer'}, - 'AcquisitionMatrix': {'type': 'string'}, - 'DeviceSerialNumber': {'type': 'string'}, - 'EchoTime': {'type': 'float'}, - 'EchoTrainLength': {'type': 'integer'}, - 'FlipAngle': {'type': 'integer'}, - 'ImageType': {'type': 'string'}, - 'ImagingFrequency': {'type': 'integer'}, - 'InPlanePhaseEncodingDirection': {'type': 'string'}, - 'InversionTime': {'type': 'float'}, - 'MRAcquisitionType': {'type': 'string'}, - 'MagneticFieldStrength': {'type': 'integer'}, - 'ManufacturerModelName': {'type': 'string'}, - 'NumberOfAverages': {'type': 'integer'}, - 'NumberOfPhaseEncodingSteps': {'type': 'integer'}, - 'PatientPosition': {'type': 'string'}, - 'PercentPhaseFieldOfView': {'type': 'integer'}, - 'PercentSampling': {'type': 'integer'}, - 'PhaseEncodingDirection': {'type': 'string'}, - 'PixelBandwidth': {'type': 'integer'}, - 'ProtocolName': {'type': 'string'}, - 'ReceiveCoilName': {'type': 'string'}, - 'RepetitionTime': {'type': 'float'}, - 'ScanOptions': {'type': 'string'}, - 'ScanningSequence': {'type': 'string'}, - 'SequenceName': {'type': 'string'}, - 'SequenceVariant': {'type': 'string'}, - 'SoftwareVersions': {'type': 'string'}, - 'TotalScanTimeSec': {'type': 'integer'}, - 'TransmitCoilName': {'type': 'string'}, - 'VariableFlipAngleFlag': {'type': 'string'}, - 'ContrastBolusIngredient': {'type': 'string'}, - 'Manufacturer': {'type': 'string'}, - 'HardcopyDeviceSoftwareVersion': {'type': 'string'}, - 'GradientSetType': {'type': 'string'}, - 'MRTransmitCoilSequence': {'type': 'string'}, - 'MatrixCoilMode': {'type': 'string'}, - 'CoilCombinationMethod': {'type': 'string'}, - 'PulseSequenceType': {'type': 'string'}, - 'PulseSequenceDetails': {'type': 'string'}, - 'NumberShots': {'type': 'integer'}, - 'ParallelReductionFactorInPlane': {'type': 'float'}, - 'ParallelAcquisitionTechnique': {'type': 'string'}, - 'PartialFourier': {'type': 'boolean'}, - 'PartialFourierDirection': {'type': 'string'}, - 'EffectiveEchoSpacing': {'type': 'float'}, - 'TotalReadoutTime': {'type': 'float'}, - 'SliceEncodingDirection': {'type': 'string'}, - 'NumberOfVolumesDiscardedByScanner': {'type': 'float'}, - 'NumberOfVolumesDiscardedByUser': {'type': 'float'}, - 'DelayTime': {'type': 'float'}, - 'MultibandAccelerationFactor': {'type': 'float'}, - 'Instructions': {'type': 'string'}, - 'TaskDescription': {'type': 'string'}, - 'CogAtlasID': {'type': 'string'}, - 'CogPOID': {'type': 'string'}, - 'InstitutionName': {'type': 'string'}, - 'InstitutionAddress': {'type': 'string'}, - 'ConversionSoftware': {'type': 'string'}, - 'ConversionSoftwareVersion': {'type': 'string'}, - } # end of schema }, # end of bold 'T1w': { 'item_title': 'T1w', 'resource_methods': ['GET', 'POST'], 'item_methods': ['GET', 'PATCH', 'PUT', 'DELETE'], - 'schema': { - # if modality == T1w, the fields below are required - 'AccelNumReferenceLines': {'type': 'integer'}, - 'AccelerationFactorPE': {'type': 'integer'}, - 'AcquisitionMatrix': {'type': 'string'}, - 'DeviceSerialNumber': {'type': 'string'}, - 'EchoTime': {'type': 'float'}, - 'EchoTrainLength': {'type': 'integer'}, - 'FlipAngle': {'type': 'integer'}, - 'ImageType': {'type': 'string'}, - 'ImagingFrequency': {'type': 'integer'}, - 'InPlanePhaseEncodingDirection': {'type': 'string'}, - 'InversionTime': {'type': 'float'}, - 'MRAcquisitionType': {'type': 'string'}, - 'MagneticFieldStrength': {'type': 'integer'}, - 'ManufacturerModelName': {'type': 'string'}, - 'NumberOfAverages': {'type': 'integer'}, - 'NumberOfPhaseEncodingSteps': {'type': 'integer'}, - 'PatientPosition': {'type': 'string'}, - 'PercentPhaseFieldOfView': {'type': 'integer'}, - 'PercentSampling': {'type': 'integer'}, - 'PhaseEncodingDirection': {'type': 'string'}, - 'PixelBandwidth': {'type': 'integer'}, - 'ProtocolName': {'type': 'string'}, - 'ReceiveCoilName': {'type': 'string'}, - 'RepetitionTime': {'type': 'float'}, - 'ScanOptions': {'type': 'string'}, - 'ScanningSequence': {'type': 'string'}, - 'SequenceName': {'type': 'string'}, - 'SequenceVariant': {'type': 'string'}, - 'SoftwareVersions': {'type': 'string'}, - 'TotalScanTimeSec': {'type': 'integer'}, - 'TransmitCoilName': {'type': 'string'}, - 'VariableFlipAngleFlag': {'type': 'string'}, - 'ContrastBolusIngredient': {'type': 'string'}, - 'Manufacturer': {'type': 'string'}, - 'HardcopyDeviceSoftwareVersion': {'type': 'string'}, - 'GradientSetType': {'type': 'string'}, - 'MRTransmitCoilSequence': {'type': 'string'}, - 'MatrixCoilMode': {'type': 'string'}, - 'CoilCombinationMethod': {'type': 'string'}, - 'PulseSequenceType': {'type': 'string'}, - 'PulseSequenceDetails': {'type': 'string'}, - 'NumberShots': {'type': 'integer'}, - 'ParallelReductionFactorInPlane': {'type': 'float'}, - 'ParallelAcquisitionTechnique': {'type': 'string'}, - 'PartialFourier': {'type': 'boolean'}, - 'PartialFourierDirection': {'type': 'string'}, - 'EffectiveEchoSpacing': {'type': 'float'}, - 'TotalReadoutTime': {'type': 'float'}, - 'SliceEncodingDirection': {'type': 'string'}, - 'NumberOfVolumesDiscardedByScanner': {'type': 'float'}, - 'NumberOfVolumesDiscardedByUser': {'type': 'float'}, - 'DelayTime': {'type': 'float'}, - 'MultibandAccelerationFactor': {'type': 'float'}, - 'Instructions': {'type': 'string'}, - 'TaskDescription': {'type': 'string'}, - 'CogAtlasID': {'type': 'string'}, - 'CogPOID': {'type': 'string'}, - 'InstitutionName': {'type': 'string'}, - 'InstitutionAddress': {'type': 'string'}, - 'ConversionSoftware': {'type': 'string'}, - 'ConversionSoftwareVersion': {'type': 'string'}, - } # end of schema } # end of T1w } } -my_settings['DOMAIN']['bold']['schema'].update(bids_schema) -my_settings['DOMAIN']['bold']['schema'].update(settings_schema) -my_settings['DOMAIN']['bold']['schema'].update(bold_iqms_schema) +my_settings['DOMAIN']['bold']['schema'] = deepcopy(bold_iqms_schema) +my_settings['DOMAIN']['bold']['schema'].update( + { + 'bids_meta': { + 'type': 'dict', + 'required': True, + 'schema': deepcopy(bids_schema) + }, + 'provenance': { + 'type': 'dict', + 'required': True, + 'schema': deepcopy(prov_schema) + } + } +) + +my_settings['DOMAIN']['bold']['schema']['bids_meta']['schema'].update({ + 'TaskName': { + 'type': 'string', + 'required': True + }, +}) + -my_settings['DOMAIN']['T1w']['schema'].update(bids_schema) -my_settings['DOMAIN']['T1w']['schema'].update(settings_schema) -my_settings['DOMAIN']['T1w']['schema'].update(t1w_iqms_schema) +my_settings['DOMAIN']['T1w']['schema'] = deepcopy(t1w_iqms_schema) +my_settings['DOMAIN']['T1w']['schema'].update( + { + 'bids_meta': { + 'type': 'dict', + 'required': True, + 'schema': deepcopy(bids_schema) + }, + 'provenance': { + 'type': 'dict', + 'required': True, + 'schema': deepcopy(prov_schema) + } + } +) diff --git a/test/T1w/validData/sub-10159_T1w.json b/test/T1w/validData/sub-10159_T1w.json deleted file mode 100755 index 955d8a1..0000000 --- a/test/T1w/validData/sub-10159_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 11.248504688892124, - "summary_bg_p95": 12.0, - "InversionTime": 1.1, - "fber": 26.33627700805664, - "DeviceSerialNumber": "35343", - "snrd_csf": 26.613233468186966, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 32.83399963378906, - "snrd_gm": 44.12607332564048, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 68.0, - "icvs_wm": 0.3610708502595193, - "RepetitionTime": 2.53, - "summary_wm_stdv": 35.2022590637207, - "snrd_wm": 60.80321593566894, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 7.911386668025524, - "icvs_gm": 0.3959101040697155, - "summary_gm_mean": 211.44973754882812, - "rpve_csf": 83261.9375, - "tpm_overlap_wm": 0.5890556573867798, - "snrd_total": 43.8475075764988, - "PixelBandwidth": 200, - "ScanningSequence": "GR/IR", - "summary_csf_p95": 170.0, - "spacing_x": 1.0, - "FlipAngle": 7, - "summary_gm_k": -0.6324611944326, - "snr_gm": 8.794440881363833, - "icvs_csf": 0.2430190456707652, - "PatientPosition": "HFS", - "SequenceName": "*tfl3d1_ns", - "summary_bg_p05": 0.0, - "ImageType": "ORIGINAL/PRIMARY/M/ND/NORM", - "qi_2": 0.0042996791690604694, - "qi_1": 5.289201412128623e-06, - "ImagingFrequency": 123249959, - "AccelerationFactorPE": 2, - "md5sum": "75cab8005361c2504ba5a7f02ecbacd7", - "ScanOptions": "IR", - "summary_csf_k": 2.800222210830917, - "wm2max": 0.6761487964989059, - "fwhm_z": 3.22984, - "fwhm_y": 3.70268, - "fwhm_x": 3.50783, - "summary_gm_p05": 167.0, - "inu_range": 0.35875076055526733, - "spacing_z": 1.0, - "spacing_y": 1.0, - "rpve_gm": 152862.53125, - "NumberOfAverages": 1, - "summary_wm_p05": 255.0, - "PhaseEncodingDirection": "i-", - "TransmitCoilName": "Body", - "modality": "T1w", - "AccelNumReferenceLines": 32, - "PercentPhaseFieldOfView": 100, - "cnr": 11.335847854614258, - "subject_id": "10159", - "inu_med": 1.2151005268096924, - "EchoTrainLength": 1, - "version": "99.99.99", - "VariableFlipAngleFlag": "N", - "efc": 0.47647998100292316, - "cjv": 0.7248942255973816, - "summary_wm_mean": 309.4393005371094, - "summary_bg_stdv": 4.799960136413574, - "summary_bg_k": 177.84711440664685, - "mriqc_pred": 1, - "ReceiveCoilName": "HeadMatrix", - "PercentSampling": 100, - "ManufacturerModelName": "TrioTim", - "summary_gm_p95": 260.0, - "EchoTime": 0.00331, - "fwhm_avg": 3.47466, - "rpve_wm": 82412.921875, - "SequenceVariant": "SP/MP", - "tpm_overlap_gm": 0.479917049407959, - "summary_csf_mean": 126.74657440185547, - "summary_bg_mean": 4.691673278808594, - "summary_wm_p95": 368.0, - "snr_csf": 3.691214433820612, - "NumberOfPhaseEncodingSteps": 255, - "summary_gm_stdv": 28.741302490234375, - "SoftwareVersions": "syngo MR B15", - "tpm_overlap_csf": 0.21703721582889557, - "summary_wm_k": -0.15745795522916461, - "software": "mriqc" -} \ No newline at end of file diff --git a/test/T1w/validData/sub-10171_T1w.json b/test/T1w/validData/sub-10171_T1w.json deleted file mode 100755 index 5d2911d..0000000 --- a/test/T1w/validData/sub-10171_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 13.063738758751342, - "summary_bg_p95": 13.0, - "InversionTime": 1.1, - "fber": 32.17710876464844, - "DeviceSerialNumber": "35343", - "snrd_csf": 17.57303577696213, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 39.63821029663086, - "snrd_gm": 30.87089348320814, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 56.0, - "icvs_wm": 0.361579551762609, - "RepetitionTime": 2.53, - "summary_wm_stdv": 41.30898666381836, - "snrd_wm": 44.23266369079579, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.11139524852314, - "icvs_gm": 0.4631067065356838, - "summary_gm_mean": 221.14871215820312, - "rpve_csf": 82997.6015625, - "tpm_overlap_wm": 0.5894558429718018, - "snrd_total": 30.892197650322018, - "PixelBandwidth": 200, - "ScanningSequence": "GR/IR", - "summary_csf_p95": 179.0, - "spacing_x": 1.0, - "FlipAngle": 7, - "summary_gm_k": -0.5402950449786084, - "snr_gm": 8.639176349636115, - "icvs_csf": 0.17531374170170722, - "PatientPosition": "HFS", - "SequenceName": "*tfl3d1_ns", - "summary_bg_p05": 0.0, - "ImageType": "ORIGINAL/PRIMARY/M/ND/NORM", - "qi_2": 0.004150545624217545, - "qi_1": 0.0, - "ImagingFrequency": 123249609, - "AccelerationFactorPE": 2, - "md5sum": "16f8ff606c121eb2c144823e2b43bb50", - "ScanOptions": "IR", - "summary_csf_k": 2.6243409438986687, - "wm2max": 0.7130801687763713, - "fwhm_z": 3.11641, - "fwhm_y": 3.5, - "fwhm_x": 3.34779, - "summary_gm_p05": 168.0, - "inu_range": 0.4733081221580506, - "spacing_z": 1.0, - "spacing_y": 1.0, - "rpve_gm": 179700.328125, - "NumberOfAverages": 1, - "summary_wm_p05": 272.0, - "PhaseEncodingDirection": "i-", - "TransmitCoilName": "Body", - "modality": "T1w", - "AccelNumReferenceLines": 32, - "PercentPhaseFieldOfView": 100, - "cnr": 8.421545028686523, - "subject_id": "10171", - "inu_med": 1.0874786376953125, - "EchoTrainLength": 1, - "version": "99.99.99", - "VariableFlipAngleFlag": "N", - "efc": 0.5185985281257072, - "cjv": 0.5742231011390686, - "summary_wm_mean": 337.3899841308594, - "summary_bg_stdv": 4.229434490203857, - "summary_bg_k": 6.201612337416636, - "mriqc_pred": 0, - "ReceiveCoilName": "HeadMatrix", - "PercentSampling": 100, - "ManufacturerModelName": "TrioTim", - "summary_gm_p95": 281.0, - "EchoTime": 0.00331, - "fwhm_avg": 3.31762, - "rpve_wm": 81151.6171875, - "SequenceVariant": "SP/MP", - "tpm_overlap_gm": 0.5497199296951294, - "summary_csf_mean": 126.52490234375, - "summary_bg_mean": 5.442507743835449, - "summary_wm_p95": 407.0, - "snr_csf": 2.631270637181967, - "NumberOfPhaseEncodingSteps": 255, - "summary_gm_stdv": 34.5344352722168, - "SoftwareVersions": "syngo MR B15", - "tpm_overlap_csf": 0.24250151216983795, - "summary_wm_k": -0.38081952750988224, - "software": "mriqc" -} \ No newline at end of file diff --git a/test/T1w/validData/sub-10189_T1w.json b/test/T1w/validData/sub-10189_T1w.json deleted file mode 100755 index 26e593c..0000000 --- a/test/T1w/validData/sub-10189_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 14.983180094093838, - "summary_bg_p95": 12.0, - "InversionTime": 1.1, - "fber": 20.806243896484375, - "DeviceSerialNumber": "35343", - "snrd_csf": 17.03981125611365, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 41.77383041381836, - "snrd_gm": 38.4512877901014, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 44.0, - "icvs_wm": 0.4137933405122368, - "RepetitionTime": 2.53, - "summary_wm_stdv": 41.74563217163086, - "snrd_wm": 55.20427248166352, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.440435733961932, - "icvs_gm": 0.41151287749321674, - "summary_gm_mean": 210.28079223632812, - "rpve_csf": 78351.65625, - "tpm_overlap_wm": 0.6125167608261108, - "snrd_total": 36.89845717595952, - "PixelBandwidth": 200, - "ScanningSequence": "GR/IR", - "summary_csf_p95": 171.0, - "spacing_x": 0.9999991655349731, - "FlipAngle": 7, - "summary_gm_k": -0.4882921239579301, - "snr_gm": 8.260903684913151, - "icvs_csf": 0.1746937819945464, - "PatientPosition": "HFS", - "SequenceName": "*tfl3d1_ns", - "summary_bg_p05": 0.0, - "ImageType": "ORIGINAL/PRIMARY/M/ND/NORM", - "qi_2": 0.004297720076594735, - 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"PercentSampling": 100, - "ManufacturerModelName": "TrioTim", - "summary_gm_p95": 273.0, - "EchoTime": 0.00331, - "fwhm_avg": 3.13198, - "rpve_wm": 78226.0859375, - "SequenceVariant": "SP/MP", - "tpm_overlap_gm": 0.5124969482421875, - "summary_csf_mean": 112.34002685546875, - "summary_bg_mean": 4.648347854614258, - "summary_wm_p95": 385.0, - "snr_csf": 2.077223422878809, - "NumberOfPhaseEncodingSteps": 255, - "summary_gm_stdv": 35.79360580444336, - "SoftwareVersions": "syngo MR B15", - "tpm_overlap_csf": 0.24477675557136536, - "summary_wm_k": -0.3090918446213582, - "software": "mriqc" -} \ No newline at end of file diff --git a/test/T1w/validData/sub-10193_T1w.json b/test/T1w/validData/sub-10193_T1w.json deleted file mode 100755 index e862c50..0000000 --- a/test/T1w/validData/sub-10193_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 11.060548636076344, - "summary_bg_p95": 14.0, - "InversionTime": 1.1, - "fber": 22.83367156982422, - "DeviceSerialNumber": "35343", - "snrd_csf": 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index 1fe3a4e..0000000 --- a/test/T1w/validData/sub-10269_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 8.612229553286955, - "summary_bg_p95": 38.0, - "InversionTime": 1.1, - "fber": 7.5888519287109375, - "DeviceSerialNumber": "35343", - "snrd_csf": 5.994926569078181, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 36.56460952758789, - "snrd_gm": 12.671962787007594, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 39.0, - "icvs_wm": 0.41281842699243415, - "RepetitionTime": 2.53, - "summary_wm_stdv": 41.44934844970703, - "snrd_wm": 17.558117052479325, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 6.099277033890897, - "icvs_gm": 0.4050560280558791, - "summary_gm_mean": 190.191162109375, - "rpve_csf": 162937.25, - "tpm_overlap_wm": 0.5883471369743347, - "snrd_total": 12.075002136188367, - "PixelBandwidth": 200, - 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newline at end of file diff --git a/test/T1w/validData/sub-10271_T1w.json b/test/T1w/validData/sub-10271_T1w.json deleted file mode 100755 index 94e3063..0000000 --- a/test/T1w/validData/sub-10271_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 14.471734158333328, - "summary_bg_p95": 11.0, - "InversionTime": 1.1, - "fber": 19.313926696777344, - "DeviceSerialNumber": "35343", - "snrd_csf": 18.564585702037796, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 29.91183853149414, - "snrd_gm": 32.631960936364905, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 50.0, - "icvs_wm": 0.37543294290180074, - "RepetitionTime": 2.53, - "summary_wm_stdv": 32.35560989379883, - "snrd_wm": 47.048918950841966, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.680462426412648, - "icvs_gm": 0.42275495947837827, - "summary_gm_mean": 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100755 index 63807c1..0000000 --- a/test/T1w/validData/sub-10292_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.604563609421312, - "summary_bg_p95": 14.0, - "InversionTime": 1.1, - "fber": 15.157873153686523, - "DeviceSerialNumber": "35343", - "snrd_csf": 21.528937793881113, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 35.65110397338867, - "snrd_gm": 34.84522109108244, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 73.0, - "icvs_wm": 0.3930004929965077, - "RepetitionTime": 2.53, - "summary_wm_stdv": 34.56499099731445, - "snrd_wm": 48.755563294620146, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.368889875650266, - "icvs_gm": 0.4074935774556759, - "summary_gm_mean": 220.90890502929688, - "rpve_csf": 81404.9765625, - "tpm_overlap_wm": 0.6039068102836609, - "snrd_total": 35.0432407265279, - "PixelBandwidth": 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No newline at end of file diff --git a/test/T1w/validData/sub-10304_T1w.json b/test/T1w/validData/sub-10304_T1w.json deleted file mode 100755 index 42e5d0d..0000000 --- a/test/T1w/validData/sub-10304_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.49480420724417, - "summary_bg_p95": 16.0, - "InversionTime": 1.1, - "fber": 34.763092041015625, - "DeviceSerialNumber": "35343", - "snrd_csf": 22.809291857768777, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 42.255157470703125, - "snrd_gm": 37.940874644577654, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 72.0, - "icvs_wm": 0.3866143610185275, - "RepetitionTime": 2.53, - "summary_wm_stdv": 44.02431106567383, - "snrd_wm": 54.38375865178805, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.853523392816358, - "icvs_gm": 0.41482928329744695, - "summary_gm_mean": 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deleted file mode 100755 index 6b1bbe6..0000000 --- a/test/T1w/validData/sub-10340_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.342214977903424, - "summary_bg_p95": 15.0, - "InversionTime": 1.1, - "fber": 18.299243927001953, - "DeviceSerialNumber": "35343", - "snrd_csf": 15.634693132385292, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 41.323917388916016, - "snrd_gm": 30.65267885816131, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 52.0, - "icvs_wm": 0.3985936398138991, - "RepetitionTime": 2.53, - "summary_wm_stdv": 42.66998291015625, - "snrd_wm": 45.40298284699755, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.53713301973369, - "icvs_gm": 0.4268726684782161, - "summary_gm_mean": 224.24639892578125, - "rpve_csf": 98742.359375, - "tpm_overlap_wm": 0.6041921377182007, - "snrd_total": 30.563451612514722, - 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newline at end of file diff --git a/test/T1w/validData/sub-10345_T1w.json b/test/T1w/validData/sub-10345_T1w.json deleted file mode 100755 index c926dc8..0000000 --- a/test/T1w/validData/sub-10345_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.070336195180804, - "summary_bg_p95": 12.0, - "InversionTime": 1.1, - "fber": 20.786996841430664, - "DeviceSerialNumber": "35343", - "snrd_csf": 20.61816227751572, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 40.163917541503906, - "snrd_gm": 38.68860783431475, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 50.0, - "icvs_wm": 0.38273673337413855, - "RepetitionTime": 2.53, - "summary_wm_stdv": 38.51491928100586, - "snrd_wm": 55.34988683907614, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.548954888411231, - "icvs_gm": 0.4388937436643369, - "summary_gm_mean": 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ee10076..0000000 --- a/test/T1w/validData/sub-10377_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 10.859452401921764, - "summary_bg_p95": 27.0, - "InversionTime": 1.1, - "fber": 29.905893325805664, - "DeviceSerialNumber": "35343", - "snrd_csf": 9.54490445281751, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 38.80289840698242, - "snrd_gm": 15.924844047616864, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 53.0, - "icvs_wm": 0.43642589690422695, - "RepetitionTime": 2.53, - "summary_wm_stdv": 37.233211517333984, - "snrd_wm": 21.301229199595195, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 7.394003718361937, - "icvs_gm": 0.39769602531942383, - "summary_gm_mean": 209.86666870117188, - "rpve_csf": 161418.46875, - "tpm_overlap_wm": 0.6124178767204285, - "snrd_total": 15.590325900009857, - "PixelBandwidth": 200, - 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end of file diff --git a/test/T1w/validData/sub-10388_T1w.json b/test/T1w/validData/sub-10388_T1w.json deleted file mode 100755 index a874996..0000000 --- a/test/T1w/validData/sub-10388_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 14.522752900865454, - "summary_bg_p95": 12.0, - "InversionTime": 1.1, - "fber": 21.679590225219727, - "DeviceSerialNumber": "35343", - "snrd_csf": 19.8700662937592, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 42.5841178894043, - "snrd_gm": 41.039779947957975, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 48.0, - "icvs_wm": 0.3805057061015326, - "RepetitionTime": 2.53, - "summary_wm_stdv": 38.87451934814453, - "snrd_wm": 57.15184188359448, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.57354744158502, - "icvs_gm": 0.4326093535293478, - "summary_gm_mean": 228.4509735107422, - 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index 7146c6f..0000000 --- a/test/T1w/validData/sub-10460_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 17.198754832451662, - "summary_bg_p95": 13.0, - "InversionTime": 1.1, - "fber": 27.31444549560547, - "DeviceSerialNumber": "35343", - "snrd_csf": 23.68914832295116, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 39.90277099609375, - "snrd_gm": 42.44125074330523, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 60.0, - "icvs_wm": 0.43206694485392666, - "RepetitionTime": 2.53, - "summary_wm_stdv": 34.9278450012207, - "snrd_wm": 59.451560626901646, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.345027971957606, - "icvs_gm": 0.38526931556785043, - "summary_gm_mean": 224.5480194091797, - "rpve_csf": 89389.328125, - "tpm_overlap_wm": 0.618362307548523, - "snrd_total": 41.86065323105268, - "PixelBandwidth": 200, - 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end of file diff --git a/test/T1w/validData/sub-10471_T1w.json b/test/T1w/validData/sub-10471_T1w.json deleted file mode 100755 index a7c2636..0000000 --- a/test/T1w/validData/sub-10471_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 16.300978252094108, - "summary_bg_p95": 14.0, - "InversionTime": 1.1, - "fber": 34.3030891418457, - "DeviceSerialNumber": "35343", - "snrd_csf": 25.36549441046908, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 47.53007507324219, - "snrd_gm": 41.9281405299067, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 73.0, - "icvs_wm": 0.37872429414995507, - "RepetitionTime": 2.53, - "summary_wm_stdv": 41.94192886352539, - "snrd_wm": 61.17674192599509, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.37137532979583, - "icvs_gm": 0.4296195451219927, - "summary_gm_mean": 274.36370849609375, - 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100755 index 9baed87..0000000 --- a/test/T1w/validData/sub-10523_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 12.874830332656668, - "summary_bg_p95": 13.0, - "InversionTime": 1.1, - "fber": 66.68931579589844, - "DeviceSerialNumber": "35343", - "snrd_csf": 19.390714476253656, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 38.68436050415039, - "snrd_gm": 34.84738367252374, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 66.0, - "icvs_wm": 0.3782027764407011, - "RepetitionTime": 2.53, - "summary_wm_stdv": 42.712120056152344, - "snrd_wm": 48.2327047222083, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.114613247887009, - "icvs_gm": 0.44090388953679377, - "summary_gm_mean": 224.53219604492188, - "rpve_csf": 97082.1171875, - "tpm_overlap_wm": 0.5913675427436829, - "snrd_total": 34.156934290328564, - 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at end of file diff --git a/test/T1w/validData/sub-10524_T1w.json b/test/T1w/validData/sub-10524_T1w.json deleted file mode 100755 index 68bed3e..0000000 --- a/test/T1w/validData/sub-10524_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 16.27775474755948, - "summary_bg_p95": 14.0, - "InversionTime": 1.1, - "fber": 41.287174224853516, - "DeviceSerialNumber": "35343", - "snrd_csf": 23.30547330715225, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 42.09703826904297, - "snrd_gm": 37.84002618329357, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 83.0, - "icvs_wm": 0.37735009364510497, - "RepetitionTime": 2.53, - "summary_wm_stdv": 38.61325454711914, - "snrd_wm": 52.3003269486274, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.56835477627689, - "icvs_gm": 0.4222695605505264, - "summary_gm_mean": 260.4830017089844, - 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a/test/T1w/validData/sub-10570_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 16.56776514269441, - "summary_bg_p95": 10.0, - "InversionTime": 1.1, - "fber": 37.84636688232422, - "DeviceSerialNumber": "35343", - "snrd_csf": 23.403514376528484, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 31.886058807373047, - "snrd_gm": 38.04083772784889, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 51.0, - "icvs_wm": 0.40078928238075107, - "RepetitionTime": 2.53, - "summary_wm_stdv": 30.108129501342773, - "snrd_wm": 55.74410277524538, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.469414866880102, - "icvs_gm": 0.40525477268359883, - "summary_gm_mean": 182.8069305419922, - "rpve_csf": 91231.90625, - "tpm_overlap_wm": 0.6004109978675842, - "snrd_total": 39.062818293207584, - "PixelBandwidth": 200, - "ScanningSequence": 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a/test/T1w/validData/sub-10575_T1w.json b/test/T1w/validData/sub-10575_T1w.json deleted file mode 100755 index 8f5eac4..0000000 --- a/test/T1w/validData/sub-10575_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 13.19747987304263, - "summary_bg_p95": 14.0, - "InversionTime": 1.1, - "fber": 27.36226463317871, - "DeviceSerialNumber": "35343", - "snrd_csf": 16.517224468293218, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 39.03511047363281, - "snrd_gm": 29.49267830397617, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 52.0, - "icvs_wm": 0.3742181989937522, - "RepetitionTime": 2.53, - "summary_wm_stdv": 42.22552490234375, - "snrd_wm": 41.95565050741902, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 7.990161817430522, - "icvs_gm": 0.44220336335079696, - "summary_gm_mean": 213.9035186767578, - "rpve_csf": 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--git a/test/T1w/validData/sub-10704_T1w.json b/test/T1w/validData/sub-10704_T1w.json deleted file mode 100755 index 5ac87b0..0000000 --- a/test/T1w/validData/sub-10704_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.28169667918563, - "summary_bg_p95": 11.0, - "InversionTime": 1.1, - "fber": 36.78193283081055, - "DeviceSerialNumber": "35343", - "snrd_csf": 19.746977318346396, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 41.929805755615234, - "snrd_gm": 41.36987914386149, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 45.0, - "icvs_wm": 0.38568532169857983, - "RepetitionTime": 2.53, - "summary_wm_stdv": 39.556602478027344, - "snrd_wm": 58.49737348515316, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.580317218902051, - "icvs_gm": 0.43576014739183316, - "summary_gm_mean": 218.6483917236328, - "rpve_csf": 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100755 index bf968f7..0000000 --- a/test/T1w/validData/sub-10762_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 15.609534876591516, - "summary_bg_p95": 11.0, - "InversionTime": 1.1, - "fber": 22.09418487548828, - "DeviceSerialNumber": "35343", - "snrd_csf": 27.35826287954249, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 37.679100036621094, - "snrd_gm": 43.846493023662696, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 71.0, - "icvs_wm": 0.38495883094156136, - "RepetitionTime": 2.53, - "summary_wm_stdv": 38.02106475830078, - "snrd_wm": 61.593905617988376, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 9.326812344940379, - "icvs_gm": 0.4314564579853093, - "summary_gm_mean": 226.8270721435547, - "rpve_csf": 77084.0234375, - "tpm_overlap_wm": 0.6119973659515381, - "snrd_total": 44.266220507064524, - 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\ No newline at end of file diff --git a/test/T1w/validData/sub-10779_T1w.json b/test/T1w/validData/sub-10779_T1w.json deleted file mode 100755 index 5308c4f..0000000 --- a/test/T1w/validData/sub-10779_T1w.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "snr_wm": 14.417667614668115, - "summary_bg_p95": 12.0, - "InversionTime": 1.1, - "fber": 75.4679946899414, - "DeviceSerialNumber": "35343", - "snrd_csf": 21.714626345782797, - "InPlanePhaseEncodingDirection": "ROW", - "summary_csf_stdv": 42.57958984375, - "snrd_gm": 39.78048811053144, - "size_x": 176, - "size_y": 256, - "size_z": 256, - "AcquisitionMatrix": "0/256/256/0", - "ProtocolName": "MPRAGE - BWM", - "summary_csf_p05": 58.0, - "icvs_wm": 0.3654532662033664, - "RepetitionTime": 2.53, - "summary_wm_stdv": 37.793312072753906, - "snrd_wm": 55.83778656238244, - "MagneticFieldStrength": 3, - "TotalScanTimeSec": 363, - "MRAcquisitionType": "3D", - "snr_total": 8.536483289861847, - "icvs_gm": 0.4497612111060642, - "summary_gm_mean": 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a/test/bold/validData/sub-ds205s09_task-view_acq-RL_run-01_bold.json b/test/bold/validData/sub-ds205s09_task-view_acq-RL_run-01_bold.json new file mode 100644 index 0000000..f407a6c --- /dev/null +++ b/test/bold/validData/sub-ds205s09_task-view_acq-RL_run-01_bold.json @@ -0,0 +1,70 @@ +{ + "aor": 0.026356712328767126, + "aqi": 0.021837604520547945, + "bids_meta": { + "EchoTime": 0.035, + "FlipAngle": 90, + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Magnetom Trio", + "PulseSequenceType": "single-shot echo-planar", + "RepetitionTime": 2.2, + "TaskName": "Passive Viewing", + "acq_id": "RL", + "modality": "bold", + "run_id": "01", + "subject_id": "ds205s09", + "task_id": "view" + }, + "dummy_trs": 0, + "dvars_nstd": 31.662730931944438, + "dvars_std": 1.2074161213888892, + "dvars_vstd": 1.1041022213888891, + "efc": 0.5117519933311242, + "fber": 1188.608642578125, + "fd_mean": 0.5706990780982846, + "fd_num": 53, + "fd_perc": 72.6027397260274, + "fwhm_avg": 2.505581514396446, + "fwhm_x": 2.352052219613526, + "fwhm_y": 2.708199677157441, + "fwhm_z": 2.4564926464183716, + "gcor": 0.0352427, + "gsr_x": 0.0006787956226617098, + "gsr_y": 0.013203471899032593, + "provenance": { + "md5sum": "aef77d492282a071a442e2cf16662ba5", + "settings": { + "fd_thres": 0.2, + "hmc_fsl": false + }, + "software": "mriqc", + "version": "4ec19cb174cd4ea799d9cecc5e6f6d3b2d1cd9fe" + }, + "size_t": 73, + "size_x": 53, + "size_y": 53, + "size_z": 27, + "snr": 5.817291462936068, + "spacing_tr": 2.200000047683716, + "spacing_x": 4.000000476837158, + "spacing_y": 4.000000476837158, + "spacing_z": 3.999999761581421, + "summary_bg_k": 156.60963033425253, + "summary_bg_mad": 4.30023193359375, + "summary_bg_mean": 27.128293991088867, + "summary_bg_median": 22.99413299560547, + "summary_bg_n": 40444.0, + "summary_bg_p05": 18.97193202972412, + "summary_bg_p95": 44.68982925415038, + "summary_bg_stdv": 19.405452728271484, + "summary_fg_k": 4.2793910631979974, + "summary_fg_mad": 109.38607788085938, + "summary_fg_mean": 810.3306274414062, + "summary_fg_median": 821.72412109375, + "summary_fg_n": 16290.0, + "summary_fg_p05": 573.1374969482422, + "summary_fg_p95": 1002.7080352783203, + "summary_fg_stdv": 141.25111389160156, + "tsnr": 39.0318603515625 +} \ No newline at end of file diff --git a/test/testGetPost.py b/test/testGetPost.py index c8d6b9a..77b58e9 100644 --- a/test/testGetPost.py +++ b/test/testGetPost.py @@ -38,7 +38,7 @@ def getRequest(post_resp, url): class TestCase(unittest.TestCase): def test_00_GETAllData(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") input_count = 0 for file_name in glob(T1wPattern): @@ -57,7 +57,7 @@ def test_00_GETAllData(self): ########## Testing Bold ############ def test_01_ConnectionStatus(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(boldPattern): with open(file_name) as fp: @@ -66,13 +66,19 @@ def test_01_ConnectionStatus(self): # POST request post_resp = requests.post( urlBold, data=json.dumps(input_data), headers=header) - self.assertTrue(post_resp.raise_for_status() is None) + + if post_resp.raise_for_status() is not None: + log.debug('Response: %s', post_resp.json()) + self.assertTrue(post_resp.raise_for_status() is None) + # GET request get_resp = requests.get(getURL(post_resp, urlBold)) - self.assertTrue(get_resp.raise_for_status() is None) + if get_resp.raise_for_status() is not None: + log.debug('Response: %s', get_resp.json()) + self.assertTrue(get_resp.raise_for_status() is None) def test_02_MissingFieldInput(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(boldMissingPattern): with open(file_name) as fp: @@ -85,22 +91,28 @@ def test_02_MissingFieldInput(self): ########## Testing T1w ############ def test_03_ConnectionStatus(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(T1wPattern): with open(file_name) as fp: input_data = json.load(fp) - # print input_data - # POST request - post_resp = requests.post( - urlT1w, data=json.dumps(input_data), headers=header) + # print input_data + # POST request + post_resp = requests.post( + urlT1w, data=json.dumps(input_data), headers=header) + + log.debug('Response: %s', post_resp.json()) + if post_resp.raise_for_status() is not None: self.assertTrue(post_resp.raise_for_status() is None) - # GET request - get_resp = requests.get(getURL(post_resp, urlT1w)) + + # GET request + get_resp = requests.get(getURL(post_resp, urlT1w)) + if get_resp.raise_for_status() is not None: + log.debug('Response: %s', get_resp.json()) self.assertTrue(get_resp.raise_for_status() is None) def test_04_MissingFieldInput(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(T1wMissingPattern): with open(file_name) as fp: @@ -113,7 +125,7 @@ def test_04_MissingFieldInput(self): ########## Cross Testing: send data to wrong end point ############ def test_05_boldDataToT1wEndPoint(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(boldPattern): with open(file_name) as fp: @@ -124,7 +136,7 @@ def test_05_boldDataToT1wEndPoint(self): self.assertTrue(post_resp.status_code == codeForInvalid) def test_06_T1wDataToBoldEndPoint(self): - log = logging.getLogger("SomeTest.testSomething") + log = logging.getLogger("mriqcwebapi") for file_name in glob(T1wPattern): with open(file_name) as fp: @@ -176,6 +188,6 @@ def test_08_boldDataValid(self): if __name__ == '__main__': logging.basicConfig(stream=sys.stderr) - logging.getLogger("SomeTest.testSomething").setLevel(logging.DEBUG) + logging.getLogger("mriqcwebapi").setLevel(logging.DEBUG) unittest.main()