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Add BIDS in test data #12

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merged 1 commit into from
Nov 20, 2024
Merged

Add BIDS in test data #12

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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -25,6 +25,8 @@ share/python-wheels/
.installed.cfg
*.egg
MANIFEST
.idea
.DS_Store

# PyInstaller
# Usually these files are written by a python script from a template
Expand Down
19 changes: 19 additions & 0 deletions tests/data/bids/.bids-validator-config.json
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{
"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": []
}
2 changes: 2 additions & 0 deletions tests/data/bids/.bidsignore
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swi/
conversion_info/
2 changes: 2 additions & 0 deletions tests/data/bids/README
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This BIDS directory was generated with Clinica v0.7.4.
More information on https://www.clinica.run
5 changes: 5 additions & 0 deletions tests/data/bids/dataset_description.json
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{
"Name": "TEST",
"BIDSVersion": "1.10.0",
"DatasetType": "raw"
}
5 changes: 5 additions & 0 deletions tests/data/bids/participants.tsv
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participant_id
sub-001
sub-002
sub-003
sub-004
6 changes: 6 additions & 0 deletions tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.json
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{
"MRAcquisitionType": "3D",
"PulseSequenceType": "RM",
"Manufacturer": "GE MEDICAL SYSTEMS",
"MagneticFieldStrength": "1.5"
}
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4 changes: 4 additions & 0 deletions tests/data/bids/sub-001/ses-M000/sub-001_ses-M000_scans.tsv
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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
52 changes: 52 additions & 0 deletions tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.json
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{
"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"
}
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6 changes: 6 additions & 0 deletions tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_T1w.json
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{
"MRAcquisitionType": "3D",
"PulseSequenceType": "GR",
"Manufacturer": "GE MEDICAL SYSTEMS",
"MagneticFieldStrength": "3.0"
}
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1 change: 1 addition & 0 deletions 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
3 changes: 3 additions & 0 deletions 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
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
53 changes: 53 additions & 0 deletions tests/data/bids/sub-001/ses-M156/dwi/sub-001_ses-M156_dwi.json
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{
"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"
}
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103 changes: 103 additions & 0 deletions tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.json
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{
"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"
}
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11 changes: 11 additions & 0 deletions tests/data/bids/sub-001/ses-M156/sub-001_ses-M156_scans.tsv
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filename scan_id mri_field acq_time
0 dwi/sub-001_ses-M156_dwi.json 1120329
1 dwi/sub-001_ses-M156_dwi.nii.gz 1120329
2 dwi/sub-001_ses-M156_dwi.bval 1120329
3 dwi/sub-001_ses-M156_dwi.bvec 1120329
4 anat/sub-001_ses-M156_FLAIR.nii.gz 1120322 3.0
5 anat/sub-001_ses-M156_FLAIR.json 1120322 3.0
6 anat/sub-001_ses-M156_T1w.nii.gz 1120324 3.0 2019-01-24
7 pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz 1121997
8 func/sub-001_ses-M156_task-rest_bold.json 1120325
9 func/sub-001_ses-M156_task-rest_bold.nii.gz 1120325
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