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Add BIDS in test data (#12)
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‎.gitignore

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@@ -25,6 +25,8 @@ share/python-wheels/
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.installed.cfg
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*.egg
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MANIFEST
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.idea
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.DS_Store
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# PyInstaller
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# Usually these files are written by a python script from a template

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

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{
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"ignore": [
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"NIFTI_UNIT",
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"INCONSISTENT_PARAMETERS",
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"SLICE_TIMING_NOT_DEFINED",
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"NIFTI_PIXDIM4",
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"BOLD_NOT_4D",
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"REPETITION_TIME_MUST_DEFINE",
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"TASK_NAME_MUST_DEFINE",
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"MISSING_SESSION",
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"INCONSISTENT_SUBJECTS",
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"SCANS_FILENAME_NOT_MATCH_DATASET",
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"CUSTOM_COLUMN_WITHOUT_DESCRIPTION",
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"NO_AUTHORS"
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],
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"warn": [],
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"error": [],
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"ignoredFiles": []
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}

‎tests/data/bids/.bidsignore

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swi/
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conversion_info/

‎tests/data/bids/README

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This BIDS directory was generated with Clinica v0.7.4.
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More information on https://www.clinica.run

‎tests/data/bids/dataset_description.json

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{
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"Name": "TEST",
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"BIDSVersion": "1.10.0",
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"DatasetType": "raw"
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}

‎tests/data/bids/participants.tsv

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participant_id
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sub-001
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sub-002
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sub-003
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sub-004

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

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{
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"MRAcquisitionType": "3D",
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"PulseSequenceType": "RM",
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"Manufacturer": "GE MEDICAL SYSTEMS",
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"MagneticFieldStrength": "1.5"
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}

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

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‎tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregavg_pet.nii.gz

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‎tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregiso_pet.nii.gz

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

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

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

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

‎tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.nii.gz

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

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{
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"MRAcquisitionType": "3D",
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"PulseSequenceType": "GR",
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"Manufacturer": "GE MEDICAL SYSTEMS",
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"MagneticFieldStrength": "3.0"
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}

‎tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_T1w.nii.gz

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

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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-001_ses-M156_dwi.bvec

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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
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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
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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-001_ses-M156_dwi.json

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

‎tests/data/bids/sub-001/ses-M156/dwi/sub-001_ses-M156_dwi.nii.gz

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

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

‎tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.nii.gz

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‎tests/data/bids/sub-001/ses-M156/pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz

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

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filename scan_id mri_field acq_time
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0 dwi/sub-001_ses-M156_dwi.json 1120329
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1 dwi/sub-001_ses-M156_dwi.nii.gz 1120329
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2 dwi/sub-001_ses-M156_dwi.bval 1120329
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3 dwi/sub-001_ses-M156_dwi.bvec 1120329
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4 anat/sub-001_ses-M156_FLAIR.nii.gz 1120322 3.0
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5 anat/sub-001_ses-M156_FLAIR.json 1120322 3.0
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6 anat/sub-001_ses-M156_T1w.nii.gz 1120324 3.0 2019-01-24
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7 pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz 1121997
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8 func/sub-001_ses-M156_task-rest_bold.json 1120325
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9 func/sub-001_ses-M156_task-rest_bold.nii.gz 1120325

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