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hw2/bids/code/bidscoin/bidsmap.yaml
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| # -------------------------------------------------------------------------------- | |
| # This is a bidsmap YAML file with the key-value mappings for the different BIDS | |
| # modalities (anat, func, dwi, etc). The modality attributes are the keys that map | |
| # onto the BIDS labels. The bidsmap data-structure should be 5 levels deep: | |
| # dict > dict > list > dict > dict | |
| # | |
| # NB: | |
| # 1) Edit the bidsmap file to your needs before feeding it to bidscoiner.py | |
| # 2) (Institute) users may create their own bidsmap_[template].yaml or | |
| # bidsmap_[sample].yaml file | |
| # | |
| # For more information, see: | |
| # https://github.com/Donders-Institute/bidscoin | |
| # https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html | |
| # -------------------------------------------------------------------------------- | |
| Options: | |
| # -------------------------------------------------------------------------------- | |
| # General options | |
| # -------------------------------------------------------------------------------- | |
| bidscoin: | |
| version: '2.3' # BIDScoin version (should correspond with the version in ../bidscoin/version.txt) | |
| bidsignore: extra_data/ # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv | |
| dcm2niix: # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info | |
| path: /usr/local/bin/ # Command to set the path to dcm2niix (note the semi-colon), e.g. module add dcm2niix/1.0.20180622; or PATH=/opt/dcm2niix/bin:$PATH; or /opt/dcm2niix/bin/ or '"C:\Program Files\dcm2niix\"' (note the quotes to deal with the whitespace) | |
| args: -b y -z y -i n # Argument string that is passed to dcm2niix. Tip: SPM users may want to use '-z n' (which produces unzipped nifti's, see dcm2niix -h for more information) | |
| PlugIns: [] | |
| # -------------------------------------------------------------------------------- | |
| # List of plugins to edit the key-value heuristics / perform additional operations | |
| # -------------------------------------------------------------------------------- | |
| #- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder | |
| PlugIn: | |
| # -------------------------------------------------------------------------------- | |
| # List of plugins to edit the key-value heuristics / perform additional operations | |
| # -------------------------------------------------------------------------------- | |
| #- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder | |
| DICOM: | |
| # -------------------------------------------------------------------------------- | |
| # DICOM key-value heuristics (DICOM fields that are mapped to the BIDS labels) | |
| # -------------------------------------------------------------------------------- | |
| subject: <<SourceFilePath>> # <<SourceFilePath>> extracts the subject label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as subject-label instead, e.g. <PatientID> | |
| session: <<SourceFilePath>> # <<SourceFilePath>> extracts the session label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as session-label instead, e.g. <StudyID> | |
| anat: # ----------------------- All anatomical series -------------------- | |
| - provenance: /data/raw/sub-TD902TD/005-T1w/TD^TD902TD_005_T1w_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: T1w | |
| SeriesDescription: T1w | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']" | |
| SequenceName: '*tfl3d1_16ns' | |
| SequenceVariant: "['SK', 'SP', 'MP']" | |
| ScanningSequence: "['GR', 'IR']" | |
| MRAcquisitionType: 3D | |
| SliceThickness: '1' | |
| FlipAngle: '9' | |
| EchoNumbers: 1 | |
| EchoTime: '2.98' | |
| RepetitionTime: '2300' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| acq: '' | |
| ce: | |
| rec: | |
| run: <<1>> | |
| mod: | |
| suffix: T1w | |
| func: # ----------------------- All functional series -------------------- | |
| - provenance: /data/raw/sub-TD902TD/006-task-music_SBRef/TD^TD902TD_006_task-music_SBRef_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-music | |
| SeriesDescription: task-music_SBRef | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" | |
| SequenceName: epfid2d1_84 | |
| SequenceVariant: "['SK', 'SS']" | |
| ScanningSequence: EP | |
| MRAcquisitionType: 2D | |
| SliceThickness: '2.5' | |
| FlipAngle: '45' | |
| EchoNumbers: 1 | |
| EchoTime: '30.2' | |
| RepetitionTime: '1070' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| suffix: sbref | |
| task: music | |
| acq: epfid2d184 | |
| ce: | |
| dir: COL | |
| rec: | |
| run: <<1>> | |
| echo: '1' | |
| - provenance: /data/raw/sub-TD902TD/007-task-music/TD^TD902TD_007_task-music_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-music | |
| SeriesDescription: task-music | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" | |
| SequenceName: epfid2d1_84 | |
| SequenceVariant: "['SK', 'SS']" | |
| ScanningSequence: EP | |
| MRAcquisitionType: 2D | |
| SliceThickness: '2.5' | |
| FlipAngle: '45' | |
| EchoNumbers: 1 | |
| EchoTime: '30.2' | |
| RepetitionTime: '1070' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| task: music | |
| acq: epfid2d184 | |
| ce: | |
| dir: COL | |
| rec: | |
| run: <<1>> | |
| echo: '1' | |
| suffix: bold | |
| - provenance: /data/raw/sub-TD902TD/008-task-music_PhysioLog/TD^TD902TD_008_task-music_PhysioLog_00927_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-music | |
| SeriesDescription: task-music_PhysioLog | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']" | |
| SequenceName: '' | |
| SequenceVariant: '' | |
| ScanningSequence: '' | |
| MRAcquisitionType: '' | |
| SliceThickness: '' | |
| FlipAngle: '' | |
| EchoNumbers: '' | |
| EchoTime: '' | |
| RepetitionTime: '' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| suffix: physio | |
| task: music | |
| acq: <SequenceName> | |
| ce: | |
| dir: <InPlanePhaseEncodingDirection> | |
| rec: | |
| run: <<1>> | |
| echo: <EchoNumbers> | |
| - provenance: /data/raw/sub-TD902TD/009-task-prosody_SBRef/TD^TD902TD_009_task-prosody_SBRef_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-prosody | |
| SeriesDescription: task-prosody_SBRef | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" | |
| SequenceName: epfid2d1_84 | |
| SequenceVariant: "['SK', 'SS']" | |
| ScanningSequence: EP | |
| MRAcquisitionType: 2D | |
| SliceThickness: '2.5' | |
| FlipAngle: '45' | |
| EchoNumbers: 1 | |
| EchoTime: '30.2' | |
| RepetitionTime: '1070' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| suffix: sbref | |
| task: prosody | |
| acq: epfid2d184 | |
| ce: | |
| dir: COL | |
| rec: | |
| run: <<1>> | |
| echo: '1' | |
| - provenance: /data/raw/sub-TD902TD/010-task-prosody/TD^TD902TD_010_task-prosody_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-prosody | |
| SeriesDescription: task-prosody | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" | |
| SequenceName: epfid2d1_84 | |
| SequenceVariant: "['SK', 'SS']" | |
| ScanningSequence: EP | |
| MRAcquisitionType: 2D | |
| SliceThickness: '2.5' | |
| FlipAngle: '45' | |
| EchoNumbers: 1 | |
| EchoTime: '30.2' | |
| RepetitionTime: '1070' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| task: prosody | |
| acq: epfid2d184 | |
| ce: | |
| dir: COL | |
| rec: | |
| run: <<1>> | |
| echo: '1' | |
| suffix: bold | |
| - provenance: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog/TD^TD902TD_011_task-prosody_PhysioLog_00046_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: task-prosody | |
| SeriesDescription: task-prosody_PhysioLog | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']" | |
| SequenceName: '' | |
| SequenceVariant: '' | |
| ScanningSequence: '' | |
| MRAcquisitionType: '' | |
| SliceThickness: '' | |
| FlipAngle: '' | |
| EchoNumbers: '' | |
| EchoTime: '' | |
| RepetitionTime: '' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| suffix: physio | |
| task: prosody | |
| acq: <SequenceName> | |
| ce: | |
| dir: <InPlanePhaseEncodingDirection> | |
| rec: | |
| run: <<1>> | |
| echo: <EchoNumbers> | |
| dwi: # ----------------------- All diffusion series --------------------- | |
| fmap: # ----------------------- All fieldmap series ---------------------- | |
| beh: # ----------------------- All behavioural data --------------------- | |
| pet: # ----------------------- All PET series --------------------------- | |
| extra_data: # ----------------------- All extra data --------------------------- | |
| - provenance: /data/raw/sub-TD902TD/001-AAHead_Scout/TD^TD902TD_001_AAHead_Scout_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: AAHead_Scout | |
| SeriesDescription: AAHead_Scout | |
| ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']" | |
| SequenceName: '*fl3d1_ns' | |
| SequenceVariant: SP | |
| ScanningSequence: GR | |
| MRAcquisitionType: 3D | |
| SliceThickness: '1.6000000238419' | |
| FlipAngle: '8' | |
| EchoNumbers: 1 | |
| EchoTime: '1.37' | |
| RepetitionTime: '3.15' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| acq: AAHeadScout | |
| rec: | |
| ce: | |
| task: | |
| echo: '1' | |
| dir: ROW | |
| run: <<1>> | |
| mod: | |
| suffix: | |
| - provenance: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag/TD^TD902TD_002_AAHead_Scout_MPR_sag_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: AAHead_Scout | |
| SeriesDescription: AAHead_Scout_MPR_sag | |
| ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" | |
| SequenceName: '*fl3d1_ns' | |
| SequenceVariant: SP | |
| ScanningSequence: GR | |
| MRAcquisitionType: 3D | |
| SliceThickness: '1.6000000238419' | |
| FlipAngle: '8' | |
| EchoNumbers: 1 | |
| EchoTime: '1.37' | |
| RepetitionTime: '3.15' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| acq: AAHeadScoutMPRsag | |
| rec: | |
| ce: | |
| task: | |
| echo: '1' | |
| dir: <InPlanePhaseEncodingDirection> | |
| run: <<1>> | |
| mod: | |
| suffix: | |
| - provenance: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor/TD^TD902TD_003_AAHead_Scout_MPR_cor_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: AAHead_Scout | |
| SeriesDescription: AAHead_Scout_MPR_cor | |
| ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" | |
| SequenceName: '*fl3d1_ns' | |
| SequenceVariant: SP | |
| ScanningSequence: GR | |
| MRAcquisitionType: 3D | |
| SliceThickness: '1.6000000238419' | |
| FlipAngle: '8' | |
| EchoNumbers: 1 | |
| EchoTime: '1.37' | |
| RepetitionTime: '3.15' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| acq: AAHeadScoutMPRcor | |
| rec: | |
| ce: | |
| task: | |
| echo: '1' | |
| dir: <InPlanePhaseEncodingDirection> | |
| run: <<1>> | |
| mod: | |
| suffix: | |
| - provenance: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra/TD^TD902TD_004_AAHead_Scout_MPR_tra_00001_00001.dcm | |
| attributes: | |
| Modality: MR | |
| ProtocolName: AAHead_Scout | |
| SeriesDescription: AAHead_Scout_MPR_tra | |
| ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" | |
| SequenceName: '*fl3d1_ns' | |
| SequenceVariant: SP | |
| ScanningSequence: GR | |
| MRAcquisitionType: 3D | |
| SliceThickness: '1.6000000238419' | |
| FlipAngle: '8' | |
| EchoNumbers: 1 | |
| EchoTime: '1.37' | |
| RepetitionTime: '3.15' | |
| PhaseEncodingDirection: '' | |
| bids: | |
| acq: AAHeadScoutMPRtra | |
| rec: | |
| ce: | |
| task: | |
| echo: '1' | |
| dir: <InPlanePhaseEncodingDirection> | |
| run: <<1>> | |
| mod: | |
| suffix: | |
| leave_out: # ----------------------- Data that will be left out --------------- | |
| PAR: | |
| # -------------------------------------------------------------------------------- | |
| # PAR key-value heuristics (Philips PAR fields that are mapped to the BIDS labels) | |
| # -------------------------------------------------------------------------------- | |
| P7: | |
| # -------------------------------------------------------------------------------- | |
| # P*.7 key-value heuristics (GE fields that are mapped to the BIDS labels) | |
| # -------------------------------------------------------------------------------- | |
| Nifti: | |
| # -------------------------------------------------------------------------------- | |
| # Nifti key-value heuristics (Nifti fields that are mapped to the BIDS labels) | |
| # -------------------------------------------------------------------------------- | |
| FileSystem: | |
| # -------------------------------------------------------------------------------- | |
| # File system key-value heuristics (these file- and foldernames will be mapped | |
| # to the BIDS labels; Special substitutions can be performed using python's | |
| # Format Specification Mini-Language) | |
| # -------------------------------------------------------------------------------- | |
| subject: <<SourceFilePath>> # <<SourceFilePath>> extracts the subject label from the source directory during bidscoiner runtime | |
| session: <<SourceFilePath>> # <<SourceFilePath>> extracts the session label from the source directory during bidscoiner runtime | |
| anat: # ----------------------- All anatomical series -------------------- | |
| func: # ----------------------- All functional series -------------------- | |
| dwi: # ----------------------- All diffusion series --------------------- | |
| fmap: # ----------------------- All fieldmap series ---------------------- | |
| beh: # ----------------------- All behavioural data --------------------- | |
| extra_data: # ----------------------- All extra data --------------------------- | |
| leave_out: # ----------------------- Data that will be left out --------------- |