Add BIDS in test data

.gitignore

@@ -25,6 +25,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+.idea
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

tests/data/bids/.bids-validator-config.json

@@ -0,0 +1,19 @@
+{
+    "ignore": [
+        "NIFTI_UNIT",
+        "INCONSISTENT_PARAMETERS",
+        "SLICE_TIMING_NOT_DEFINED",
+        "NIFTI_PIXDIM4",
+        "BOLD_NOT_4D",
+        "REPETITION_TIME_MUST_DEFINE",
+        "TASK_NAME_MUST_DEFINE",
+        "MISSING_SESSION",
+        "INCONSISTENT_SUBJECTS",
+        "SCANS_FILENAME_NOT_MATCH_DATASET",
+        "CUSTOM_COLUMN_WITHOUT_DESCRIPTION",
+        "NO_AUTHORS"
+    ],
+    "warn": [],
+    "error": [],
+    "ignoredFiles": []
+}

tests/data/bids/.bidsignore

@@ -0,0 +1,2 @@
+swi/
+conversion_info/

tests/data/bids/README

@@ -0,0 +1,2 @@
+This BIDS directory was generated with Clinica v0.7.4.
+More information on https://www.clinica.run

tests/data/bids/dataset_description.json

@@ -0,0 +1,5 @@
+{
+    "Name": "TEST",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "raw"
+}

tests/data/bids/participants.tsv

@@ -0,0 +1,5 @@
+participant_id
+sub-001
+sub-002
+sub-003
+sub-004

tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.json

@@ -0,0 +1,6 @@
+{
+    "MRAcquisitionType": "3D",
+    "PulseSequenceType": "RM",
+    "Manufacturer": "GE MEDICAL SYSTEMS",
+    "MagneticFieldStrength": "1.5"
+}

tests/data/bids/sub-001/ses-M000/sub-001_ses-M000_scans.tsv

@@ -0,0 +1,4 @@
+	filename	scan_id	mri_field	acq_time
+0	anat/sub-001_ses-M000_T1w.nii.gz	34316	1.5	2005-12-09
+1	pet/sub-001_ses-M000_trc-18FFDG_rec-coregavg_pet.nii.gz	26939		
+2	pet/sub-001_ses-M000_trc-18FFDG_rec-coregiso_pet.nii.gz	26939		

tests/data/bids/sub-001/ses-M156/anat/sub-ADNI027S0074_ses-M156_FLAIR.json

@@ -0,0 +1,52 @@
+{
+    "Modality": "MR",
+    "ImagingFrequency": 127.704,
+    "PulseSequenceName": "CubeT2flair",
+    "ManufacturersModelName": "DISCOVERY MR750",
+    "InstitutionName": "UIRR",
+    "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk",
+    "BodyPartExamined": "BRAIN",
+    "PatientPosition": "HFS",
+    "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a",
+    "SeriesDescription": "Sagittal 3D FLAIR",
+    "ProtocolName": "ADNI3 Basic Human Protoc",
+    "ScanningSequence": "SE\\IR",
+    "SequenceVariant": "SK",
+    "ScanOptions": "SAT_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS\\FS",
+    "ImageType": [
+        "ORIGINAL",
+        "PRIMARY",
+        "OTHER"
+    ],
+    "SeriesNumber": 5,
+    "AcquisitionTime": "10:16:36.000000",
+    "AcquisitionNumber": 1,
+    "SliceThickness": 1.2,
+    "SpacingBetweenSlices": 1.2,
+    "SAR": 0.718189,
+    "EchoTime": 0.11668,
+    "RepetitionTime": 4.8,
+    "InversionTime": 1.476,
+    "FlipAngle": 90,
+    "CoilString": "8HRBRAIN",
+    "PercentPhaseFOV": 100,
+    "PercentSampling": 100,
+    "EchoTrainLength": 182,
+    "AcquisitionMatrixPE": 256,
+    "ReconMatrixPE": 256,
+    "ParallelReductionFactorInPlane": 2,
+    "ParallelReductionOutOfPlane": 2,
+    "PixelBandwidth": 244.141,
+    "PhaseEncodingAxis": "i",
+    "ImageOrientationPatientDICOM": [
+        0,
+        1,
+        0,
+        0,
+        0,
+        -1
+    ],
+    "InPlanePhaseEncodingDirectionDICOM": "ROW",
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20220505"
+}

tests/data/bids/sub-001/ses-M156/anat/sub-ADNI027S0074_ses-M156_T1w.json

@@ -0,0 +1,6 @@
+{
+    "MRAcquisitionType": "3D",
+    "PulseSequenceType": "GR",
+    "Manufacturer": "GE MEDICAL SYSTEMS",
+    "MagneticFieldStrength": "3.0"
+}

tests/data/bids/sub-001/ses-M156/dwi/sub-ADNI027S0074_ses-M156_dwi.bval

@@ -0,0 +1 @@
+0 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

tests/data/bids/sub-001/ses-M156/dwi/sub-ADNI027S0074_ses-M156_dwi.bvec

@@ -0,0 +1,3 @@
+0 0 0 0 0 0 -1 -0.48 0.155 -0.942 -0.029 0.635 -0.504 -0.135 -0.759 0.031 -0.11 -0.377 0.31 0.57 0.643 0.768 -0.749 -0.421 0.257 0.778 -0.612 0.518 -0.93 -0.405 0.193 -0.318 -0.915 -0.215 0.557 -0.946 0.303 0.06 0.252 0.621 0.864 0.932 -0.643 0.338 -0.823 0.375 -0.661 -0.031 0.608 0.015 -0.806 0.279 0.383 -0.812
+0 0 0 0 0 0 0 0.877 0.466 -0.303 -0.482 -0.149 0.337 0.99 0.261 -0.959 -0.944 -0.692 -0.713 0.752 0.035 -0.64 -0.151 -0.249 -0.899 0.572 0.724 0.356 0.058 0.687 -0.513 -0.894 0.039 -0.201 0.672 0.324 0.644 0.021 -0.169 -0.439 -0.349 0.262 -0.765 0.937 0.464 -0.075 0.652 -0.8 0.469 0.776 -0.285 -0.406 -0.864 -0.518
+0 0 0 0 0 0 0 0 0.871 0.146 0.876 0.758 0.795 0.042 0.596 0.283 -0.312 -0.616 0.629 0.331 -0.765 0.032 -0.645 -0.872 -0.356 -0.258 0.318 -0.778 0.364 0.604 -0.836 0.315 -0.402 0.956 -0.487 -0.003 -0.703 0.998 -0.953 0.649 0.364 0.25 0.042 0.085 0.327 0.924 -0.372 0.599 0.64 0.63 0.519 0.87 0.328 -0.269

tests/data/bids/sub-001/ses-M156/dwi/sub-ADNI027S0074_ses-M156_dwi.json

@@ -0,0 +1,53 @@
+{
+    "Modality": "MR",
+    "ImagingFrequency": 127.704,
+    "PulseSequenceName": "epi2",
+    "InternalPulseSequenceName": "EPI2",
+    "ManufacturersModelName": "DISCOVERY MR750",
+    "InstitutionName": "UIRR",
+    "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk",
+    "BodyPartExamined": "BRAIN",
+    "PatientPosition": "HFS",
+    "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a",
+    "SeriesDescription": "Axial DTI",
+    "ProtocolName": "ADNI3 Basic Human Protoc",
+    "ScanningSequence": "EP\\SE",
+    "SequenceVariant": "NONE",
+    "ScanOptions": "SAT_GEMS\\EPI_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFF\\FS",
+    "ImageType": [
+        "ORIGINAL",
+        "PRIMARY",
+        "OTHER"
+    ],
+    "SeriesNumber": 8,
+    "AcquisitionTime": "10:35:14.000000",
+    "AcquisitionNumber": 1,
+    "SliceThickness": 2,
+    "SpacingBetweenSlices": 2,
+    "SAR": 0.700869,
+    "EchoTime": 0.0604,
+    "RepetitionTime": 7.8,
+    "FlipAngle": 90,
+    "PhaseEncodingPolarityGE": "Flipped",
+    "CoilString": "8HRBRAIN",
+    "PercentPhaseFOV": 100,
+    "PercentSampling": 100,
+    "AcquisitionMatrixPE": 116,
+    "ReconMatrixPE": 256,
+    "ParallelReductionFactorInPlane": 2,
+    "EffectiveEchoSpacing": 0.000158259,
+    "TotalReadoutTime": 0.040356,
+    "PixelBandwidth": 1953.12,
+    "PhaseEncodingDirection": "j",
+    "ImageOrientationPatientDICOM": [
+        1,
+        0,
+        0,
+        0,
+        1,
+        0
+    ],
+    "InPlanePhaseEncodingDirectionDICOM": "COL",
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20220505"
+}

tests/data/bids/sub-001/ses-M156/func/sub-ADNI027S0074_ses-M156_task-rest_bold.json

@@ -0,0 +1,103 @@
+{
+    "Modality": "MR",
+    "ImagingFrequency": 127.704,
+    "PulseSequenceName": "epi",
+    "InternalPulseSequenceName": "EPI",
+    "ManufacturersModelName": "DISCOVERY MR750",
+    "InstitutionName": "UIRR",
+    "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk",
+    "BodyPartExamined": "BRAIN",
+    "PatientPosition": "HFS",
+    "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a",
+    "SeriesDescription": "Axial rsfMRI (Eyes Open)",
+    "ProtocolName": "ADNI3 Basic Human Protoc",
+    "ScanningSequence": "EP\\GR",
+    "SequenceVariant": "SS",
+    "ScanOptions": "MP_GEMS\\EPI_GEMS",
+    "ImageType": [
+        "ORIGINAL",
+        "PRIMARY",
+        "OTHER"
+    ],
+    "SeriesNumber": 9,
+    "AcquisitionTime": "10:43:51.000000",
+    "AcquisitionNumber": 1,
+    "TriggerDelayTime": 599938,
+    "SliceThickness": 3.4,
+    "SpacingBetweenSlices": 3.4,
+    "SAR": 0.338675,
+    "EchoTime": 0.03,
+    "RepetitionTime": 3,
+    "FlipAngle": 90,
+    "PhaseEncodingPolarityGE": "Flipped",
+    "CoilString": "8HRBRAIN",
+    "PercentPhaseFOV": 100,
+    "PercentSampling": 100,
+    "AcquisitionMatrixPE": 64,
+    "ReconMatrixPE": 64,
+    "EffectiveEchoSpacing": 0.000416,
+    "TotalReadoutTime": 0.026208,
+    "PixelBandwidth": 7812.5,
+    "PhaseEncodingDirection": "j",
+    "SliceTiming": [
+        0,
+        1.5,
+        0.0625,
+        1.5625,
+        0.125,
+        1.625,
+        0.1875,
+        1.6875,
+        0.25,
+        1.75,
+        0.3125,
+        1.8125,
+        0.375,
+        1.875,
+        0.4375,
+        1.9375,
+        0.5,
+        2,
+        0.5625,
+        2.0625,
+        0.625,
+        2.125,
+        0.6875,
+        2.1875,
+        0.75,
+        2.25,
+        0.8125,
+        2.3125,
+        0.875,
+        2.375,
+        0.9375,
+        2.4375,
+        1,
+        2.5,
+        1.0625,
+        2.5625,
+        1.125,
+        2.625,
+        1.1875,
+        2.6875,
+        1.25,
+        2.75,
+        1.3125,
+        2.8125,
+        1.375,
+        2.875,
+        1.4375,
+        2.9375
+    ],
+    "ImageOrientationPatientDICOM": [
+        1,
+        0,
+        0,
+        0,
+        1,
+        0
+    ],
+    "InPlanePhaseEncodingDirectionDICOM": "COL",
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20220505"
+}

tests/data/bids/sub-001/ses-M156/sub-ADNI027S0074_ses-M156_scans.tsv

@@ -0,0 +1,11 @@
+	filename	scan_id	mri_field	acq_time
+0	dwi/sub-ADNI027S0074_ses-M156_dwi.json	1120329		
+1	dwi/sub-ADNI027S0074_ses-M156_dwi.nii.gz	1120329		
+2	dwi/sub-ADNI027S0074_ses-M156_dwi.bval	1120329		
+3	dwi/sub-ADNI027S0074_ses-M156_dwi.bvec	1120329		
+4	anat/sub-ADNI027S0074_ses-M156_FLAIR.nii.gz	1120322	3.0	
+5	anat/sub-ADNI027S0074_ses-M156_FLAIR.json	1120322	3.0	
+6	anat/sub-ADNI027S0074_ses-M156_T1w.nii.gz	1120324	3.0	2019-01-24
+7	pet/sub-ADNI027S0074_ses-M156_trc-18FAV45_pet.nii.gz	1121997		
+8	func/sub-ADNI027S0074_ses-M156_task-rest_bold.json	1120325		
+9	func/sub-ADNI027S0074_ses-M156_task-rest_bold.nii.gz	1120325