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bidsmap_sst.yaml
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bidsmap_sst.yaml
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# --------------------------------------------------------------------------------
# This is a template bidsmap with the key-value mappings for the different BIDS
# datatypes (anat, func, dwi, etc). The datatype attributes are the keys that map
# onto the BIDS labels. The bidsmap data-structure should be 5 levels deep:
#
# dict : dict : list : dict : dict
# dataformat : datatype : run-item : bidsmapping : mapping-data
#
# NB:
# 1) This bidsmap is intended to be used by the bidsmapper for data discovery.
# Although generally not recommended, it can also be used directly by the bidscoiner
# 2) This bidsmap is tailored for use within the Scan Session Tool
# (https://github.com/fladd/ScanSessionTool)
#
# For more information, see: https://bidscoin.readthedocs.io
# --------------------------------------------------------------------------------
$schema: schema.json
Options:
# --------------------------------------------------------------------------------
# General BIDScoin and plugin options
# --------------------------------------------------------------------------------
bidscoin:
version: 4.3.2+qt5 # BIDScoin version (should correspond with the version in pyproject.toml)
subprefix: sub- # The subject prefix of the source data
sesprefix: ses- # The session prefix of the source data
bidsignore: [mrs/, extra_data/, sub-*_ct.*] # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]
unknowntypes: [mrs, extra_data] # A list of datatypes that are converted to BIDS-like datatype folders
ignoretypes: [exclude] # A list of datatypes that are excluded / not converted to BIDS
notderivative: [] # A list of suffixes that should not be considered as a derivative datatype
unzip: # Wildcard pattern to select tarball/zip-files in the source folders that need to be unzipped (in a tempdir) to expose the data, e.g. '*.tar.gz'
plugins: # List of plugins with plugin-specific key-value pairs (that can be used by the plugin)
dcm2niix2bids: # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info
command: dcm2niix # Command to run dcm2niix, e.g. "module add dcm2niix/1.0.20180622; dcm2niix" or "PATH=/opt/dcm2niix/bin:$PATH; dcm2niix" or /opt/dcm2niix/bin/dcm2niix or 'C:\"Program Files"\dcm2niix\dcm2niix.exe' (use quotes to deal with whitespaces in the path)
args: -b y -z y -i n -l 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)
anon: y # Set this anonymization flag to 'y' to round off age and discard acquisition date from the meta data
meta: [.json, .tsv, .tsv.gz] # The file extensions of the equally named metadata sourcefiles that are copied over to the BIDS sidecar files
fallback: y # Appends unhandled dcm2niix suffixes to the `acq` label if 'y' (recommended, else the suffix data is discarded)
DICOM:
# --------------------------------------------------------------------------------
# DICOM key-value heuristics (DICOM fields that are mapped to the BIDS labels)
# --------------------------------------------------------------------------------
subject: <<filepath:/sub-(.*?)/>> # This filesystem property extracts the subject label from the source directory. NB: Any property or attribute can be used as subject-label, e.g. <PatientID>
session: <<filepath:/sub-.*?/ses-\.\.\.(.*?)/>> # This filesystem property extracts the subject label from the source directory. NB: Any property or attribute can be used as session-label, e.g. <StudyID>
anat: # ----------------------- All anatomical runs --------------------
- provenance: # The fullpath name of the DICOM file from which the attributes are read. Serves also as a look-up key to find a run in the bidsmap
properties: &fileprop # This is an optional (stub) entry of properties matching (could be added to any run-item)
filepath: # File folder, e.g. ".*/Parkinson/.*" or ".*(phantom|bottle).*"
filename: # File name, e.g. ".*fmap.*" or ".*(fmap|field.?map|B0.?map).*"
filesize: # File size, e.g. "2[4-6]\d MB" for matching files between 240-269 MB
nrfiles: # Number of files in the folder
attributes: &anat_dicomattr # An empty / non-matching reference dictionary that can be dereferenced in other run-items of this data type
Modality:
ProtocolName:
SeriesDescription:
ImageType:
SequenceName:
PulseSequenceName:
SequenceVariant:
ScanningSequence:
EchoPulseSequence: # Enhanced DICOM
MRAcquisitionType:
SliceThickness:
FlipAngle:
EchoNumbers:
EchoTime:
EffectiveEchoTime:
RepetitionTime:
InPlanePhaseEncodingDirection:
bids: &anat_dicoment_nonparametric # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/> # This will be expanded by the bidsmapper (so the user can edit it in the bidseditor)
ce:
rec:
run: <<>> # This will be updated dynamically during bidscoiner runtime (as it depends on the already existing files)
echo:
part: ['', mag, phase, real, imag, 0] # # This BIDS value list will be shown as a dropdown menu in the bidseditor with the first (empty) item selected (as indicated by the last item, i.e. 0)
chunk:
suffix: T1w
meta: {} # This is an optional entry for meta-data that will be appended to the json sidecar files produced by the plugin
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*(MPRAGE|T1w).*
MRAcquisitionType: 3D
bids: *anat_dicoment_nonparametric
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T2w.*
SequenceVariant: "['SK', 'SP']"
bids:
<<: *anat_dicoment_nonparametric
suffix: T2w
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*TSE.*vfl.*
ImageType: .*'NORM'.* # NB: The non-NORM image is saved in 'extra_data'
bids:
<<: *anat_dicoment_nonparametric
suffix: T2w
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: .*PDw.*
bids:
<<: *anat_dicoment_nonparametric
suffix: PDw
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T2star.*
bids:
<<: *anat_dicoment_nonparametric
suffix: T2starw
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*FLAIR.*
bids:
<<: *anat_dicoment_nonparametric
suffix: FLAIR
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*Inplane.?T1.*
bids:
<<: *anat_dicoment_nonparametric
suffix: inplaneT1
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*Inplane.?T2.*
bids:
<<: *anat_dicoment_nonparametric
suffix: inplaneT2
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: .*PDT2.*
bids:
<<: *anat_dicoment_nonparametric
suffix: PDT2
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*ANGIO.*
bids:
<<: *anat_dicoment_nonparametric
suffix: angio
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T1.?map.*
bids: &anat_dicoment_parametric # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
chunk:
suffix: T1map
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T2.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: T2map
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T2star.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: T2starmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*R1.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: R1map
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*R2.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: R2map
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*R2star.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: R2starmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*PD.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: PDmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MTR.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: MTRmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MT.?sat.*
bids:
<<: *anat_dicoment_parametric
suffix: MTsat
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MP2RAGE.*
SeriesDescription: (?i).*UNI.*
MRAcquisitionType: 3D
bids:
<<: *anat_dicoment_parametric
suffix: UNIT1
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*T1rho.*
bids:
<<: *anat_dicoment_parametric
suffix: T1rho
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MWF.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: MWFmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MTV.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: MTVmap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*Chi.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: Chimap
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*S0.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: S0map
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*M0.?map.*
bids:
<<: *anat_dicoment_parametric
suffix: M0map
- provenance:
attributes: *anat_dicomattr
bids: &anat_dicoment_defacemask # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
mod:
chunk:
suffix: defacemask
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*ME.?SE.*
bids: &anat_dicoment_multiecho # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
echo: <EchoNumbers>
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: MESE
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*ME.?GRE.*
bids:
<<: *anat_dicoment_multiecho
suffix: MEGRE
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*VFA.*
bids: &anat_dicoment_multiflip # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
echo: <EchoNumbers>
run: <<>>
flip:
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: VFA
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*IR.?T1.*
bids: &anat_dicoment_multiinv # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
inv:
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: IRT1
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MP2RAGE.*
SeriesDescription: (?i).*INV1.*
MRAcquisitionType: 3D
bids: &anat_dicoment_mp2rage # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
echo:
flip:
inv: 1
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: MP2RAGE
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MP2RAGE.*
SeriesDescription: (?i).*INV2.*
MRAcquisitionType: 3D
bids:
<<: *anat_dicoment_mp2rage
inv: 2
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MPM.*
EffectiveEchoTime:
bids: &anat_dicoment_vfamt # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
echo:
flip:
mt:
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: MPM
meta:
EffectiveEchoTime: <<EffectiveEchoTime>>
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MTS.*
bids:
<<: *anat_dicoment_vfamt
suffix: MTS
- provenance:
attributes:
<<: *anat_dicomattr
ProtocolName: (?i).*MTR.*
bids: &anat_dicoment_mtr # See: schema/datatypes/anat.yaml
task:
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
mt:
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: MTR
- provenance: # ----------- Experimental CT support (see BEP024) -------------
attributes: &ct_dicomattr # An empty / non-matching reference dictionary that can be dereferenced in other run-items of this data type
Modality: CT
ProtocolName:
SeriesDescription:
ImageType:
PixelSpacing:
Rows:
Columns:
SliceThickness:
bids: &ct_dicoment_nonparametric
acq: <SeriesDescription> # This will be expanded by the bidsmapper (so the user can edit it in the bidseditor)
ce:
rec:
run: <<>> # This will be updated dynamically during bidscoiner runtime (as it depends on the already existing files)
chunk:
suffix: ct
func: # ----------------------- All functional runs --------------------
- provenance: # The first item with empty attributes will not match anything but is used by default when changing datatype in the bidseditor GUI -> suffix = bold
attributes: &func_dicomattr
Modality:
ProtocolName:
SeriesDescription:
ImageType:
SequenceName:
PulseSequenceName:
SequenceVariant:
ScanningSequence:
EchoPulseSequence: # Enhanced DICOM
MRAcquisitionType:
SliceThickness:
FlipAngle:
EchoNumbers:
EchoTime:
EffectiveEchoTime:
RepetitionTime:
PhaseEncodingDirection:
bids: &func_dicoment_func # See: schema/datatypes/func.yaml
task: <filepath:/.*/...(.*)/.*/>
acq:
ce:
dir: <PhaseEncodingDirection> # PhaseEncodingDirection is not an existing DICOM tag but parsed from other fields by BIDScoin
rec:
run: <<>>
echo: # Or use <EchoNumbers>
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: bold
meta: &func_meta
TaskName: <filepath:/.*/...(.*)/.*/>
B0FieldSource:
B0FieldIdentifier:
- provenance: # First match the SBREF bold runs (the normal bold runs don't have SBREF in the seriesdescription)
attributes:
<<: *func_dicomattr
SeriesDescription: (?i).*(f.?MRI|task|BOLD|func|rest|RSN|CMRR.*_TR).*SBREF.*
bids:
<<: *func_dicoment_func
suffix: sbref
meta: *func_meta
- provenance:
attributes:
<<: *func_dicomattr
ImageType: .*'FMRI'.* # XA-30 Enhanced DICOM
SeriesDescription: (?i).*SBREF.*
bids:
<<: *func_dicoment_func
suffix: sbref
meta: *func_meta
- provenance: # Then match the PHYSIO runs (the normal bold runs don't have PHYSIO in the seriesdescription)
attributes:
<<: *func_dicomattr
ProtocolName: (?i).*(f.?MRI|task|BOLD|func|rest|RSN|CMRR.*_TR).*
ImageType: .*'PHYSIO'.*
bids: &func_dicoment_timeseries # See: schema/datatypes/func.yaml
task: <filepath:/.*/...(.*)/.*/>
acq:
ce:
dir:
rec:
recording:
run: <<>>
chunk:
suffix: physio
meta:
TaskName: <filepath:/.*/...(.*)/.*/>
- provenance:
attributes:
<<: *func_dicomattr
SeriesDescription: (?i).*(f.?MRI|task|BOLD|func|rest|RSN|CMRR.*_TR).*PHYSIO.*
bids: *func_dicoment_timeseries
meta: *func_meta
- provenance: # Then catch the bold runs themselves
attributes:
<<: *func_dicomattr
ProtocolName: (?i).*(f.?MRI|task|BOLD|func|rest|RSN|CMRR.*_TR).*
bids: *func_dicoment_func
meta: *func_meta
- provenance:
attributes:
<<: *func_dicomattr
ImageType: .*'FMRI'.* # XA-30 Enhanced DICOM
bids: *func_dicoment_func
meta: *func_meta
- provenance:
attributes:
<<: *func_dicomattr
ProtocolName: (?i).*(CBV|CerebralBloodVolume).*
bids:
<<: *func_dicoment_func
suffix: cbv
meta: *func_meta
- provenance:
attributes: *func_dicomattr
bids: &func_dicoment_events # See: schema/datatypes/func.yaml
task: <filepath:/.*/...(.*)/.*/> # NB: <ProtocolName> is consistent between SBREF and PHYSIO files but causes name clashes
acq:
ce:
dir:
rec:
run: <<>>
chunk:
suffix: events
meta:
TaskName: <filepath:/.*/...(.*)/.*/>
- provenance:
attributes: *func_dicomattr
bids:
<<: *func_dicoment_timeseries
suffix: stim
meta:
TaskName: <filepath:/.*/...(.*)/.*/>
perf: # ----------------------- All perfusion runs ---------------------
- provenance:
attributes: &perf_dicomattr
Modality:
ProtocolName:
SeriesDescription:
ImageType:
SequenceName:
PulseSequenceName:
SequenceVariant:
ScanningSequence:
EchoPulseSequence: # Enhanced DICOM
MRAcquisitionType:
SliceThickness:
FlipAngle:
EchoNumbers:
EchoTime:
EffectiveEchoTime:
RepetitionTime:
PhaseEncodingDirection:
bids: &perf_dicoment_group1 # See: schema/datatypes/perf.yaml
acq: <filepath:/.*/...(.*)/.*/>
rec: <SeriesDescription>
dir: <PhaseEncodingDirection> # PhaseEncodingDirection is not an existing DICOM tag but parsed from other fields by BIDScoin
run: <<>>
suffix: asl
meta: &perf_meta
ArterialSpinLabelingType: "CASL / PCASL / PASL"
PostLabelingDelay:
BackgroundSuppression:
M0Type: "Separate / Included / Estimate / Absent"
RepetitionTimePreparation:
VascularCrushing:
AcquisitionVoxelSize:
B0FieldSource:
B0FieldIdentifier:
- provenance:
attributes:
<<: *perf_dicomattr
ProtocolName: (?i).*(ASL|Perfusion).*
bids: *perf_dicoment_group1
meta: *perf_meta
- provenance:
attributes:
<<: *perf_dicomattr
ProtocolName: (?i).*M0.?scan.*
bids:
<<: *perf_dicoment_group1
suffix: m0scan
meta: *perf_meta
- provenance:
attributes: *perf_dicomattr
bids: &perf_dicoment_group2 # See: schema/datatypes/perf.yaml
acq: <filepath:/.*/...(.*)/.*/>
rec: <SeriesDescription>
dir:
run: <<>>
suffix: aslcontext
meta: *perf_meta
- provenance:
attributes: *perf_dicomattr
bids: &perf_dicoment_group3 # See: schema/datatypes/perf.yaml
acq: <filepath:/.*/...(.*)/.*/>
rec: <SeriesDescription>
run: <<>>
suffix: asllabeling
meta: *perf_meta
# - provenance:
# attributes: *perf_dicomattr
# bids: &perf_dicoment_physio # See: schema/datatypes/perf.yaml
# acq: <filepath:/.*/...(.*)/.*/>
# rec:
# task: <SeriesDescription>
# recording:
# dir:
# run: <<>>
# suffix: physio
# meta: *perf_meta
dwi: # ----------------------- All diffusion runs ---------------------
- provenance: # The first item with empty attributes will not match anything but is used by default when changing datatype in the bidseditor GUI -> suffix = dwi
attributes: &dwi_dicomattr
Modality:
ProtocolName:
SeriesDescription:
ImageType:
SequenceName:
PulseSequenceName:
SequenceVariant:
ScanningSequence:
EchoPulseSequence: # Enhanced DICOM
MRAcquisitionType:
SliceThickness:
FlipAngle:
EchoNumbers:
EchoTime:
EffectiveEchoTime:
RepetitionTime:
PhaseEncodingDirection:
bids: &dwi_dicoment_DWI # See: schema/datatypes/dwi.yaml
acq: <filepath:/.*/...(.*)/.*/> # More consistent between SBREF and PHYSIO files
rec:
dir: <PhaseEncodingDirection> # PhaseEncodingDirection is not an existing DICOM tag but parsed from other fields by BIDScoin
run: <<>>
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: dwi
meta: &dwi_meta
B0FieldSource:
B0FieldIdentifier:
- provenance: # First match the SBREF dwi runs (the normal dwi runs don't have SBREF in the seriesdescription)
attributes:
<<: *dwi_dicomattr
SeriesDescription: (?i).*(DWI|diffusion|HARDI|DTI|dMRI|DW.?MRI).*SBREF.*
bids: &dwi_dicoment_sbref # See: schema/datatypes/dwi.yaml
acq: <filepath:/.*/...(.*)/.*/>
rec:
dir: <PhaseEncodingDirection> # PhaseEncodingDirection is not an existing DICOM tag but parsed from other fields by BIDScoin
run: <<>>
part: ['', mag, phase, real, imag, 0]
chunk:
suffix: sbref
meta: *dwi_meta
- provenance: # Then match the PHYSIO runs (the normal bold runs don't have PHYSIO in the seriesdescription)
attributes:
<<: *dwi_dicomattr
ProtocolName: (?i).*(DWI|diffusion|HARDI|DTI|dMRI|DW.?MRI).*
ImageType: .*'PHYSIO'.*
bids: &dwi_dicoment_physio # See: schema/datatypes/dwi.yaml
acq: <filepath:/.*/...(.*)/.*/>
dir:
run: <<>>
part: ['', mag, phase, real, imag, 0]
recording:
chunk:
suffix: physio
- provenance:
attributes:
<<: *dwi_dicomattr
SeriesDescription: (?i).*(DWI|diffusion|HARDI|DTI|dMRI|DW.?MRI).*PHYSIO.*
bids: *dwi_dicoment_physio
- provenance: # Then catch the normal DWI runs
attributes:
<<: *dwi_dicomattr
ProtocolName: (?i).*(DWI|diffusion|HARDI|DTI|dMRI|DW.?MRI).*
bids: *dwi_dicoment_DWI
meta: *dwi_meta
- provenance:
attributes:
<<: *dwi_dicomattr
ImageType: .*'DIFFUSION'.*
bids: *dwi_dicoment_DWI
meta: *dwi_meta
fmap: # ----------------------- All fieldmap runs ----------------------
- provenance: # The first item with empty attributes will not match anything but is used by default when changing datatype in the bidseditor GUI -> suffix = magnitude
attributes: &fmap_dicomattr
Modality:
ProtocolName:
SeriesDescription:
ImageType:
SequenceName:
PulseSequenceName:
SequenceVariant:
ScanningSequence:
EchoPulseSequence: # Enhanced DICOM
MRAcquisitionType:
SliceThickness:
FlipAngle:
EchoNumbers:
EchoTime:
EffectiveEchoTime:
RepetitionTime:
PhaseEncodingDirection:
bids: &fmap_dicoment_fieldmaps # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/>
run: <<>>
chunk:
suffix: magnitude1
meta: &fmap_meta
B0FieldIdentifier:
IntendedFor: <<bold>>
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
EchoNumbers: '2'
ImageType: .*'P'.*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: phasediff
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
EchoNumbers: '1'
ImageType: .*'M'.*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: magnitude1
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
EchoNumbers: '2'
ImageType: .*'M'.*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: magnitude2
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
EchoNumbers: '1'
ImageType: .*'P'.*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: phase1
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
EchoNumbers: '2'
ImageType: .*'P'.*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: phase2
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: fieldmap
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(fmap|field.?map|B0.?map).*
bids:
<<: *fmap_dicoment_fieldmaps
suffix: magnitude
meta: *fmap_meta
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(inverted|pepolar|_inv).*
ScanningSequence: EP
bids: &fmap_dicoment_PEPolar # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/> # NB: <ProtocolName> is consistent between SBREF and PHYSIO files but causes name clashes
ce:
dir: <PhaseEncodingDirection> # PhaseEncodingDirection is not an existing DICOM tag but parsed from other fields by BIDScoin
run: <<>>
chunk:
suffix: epi
meta: *fmap_meta
- provenance: # Siemens XA30 enhanced DICOM
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*(inverted|pepolar|_inv).*
EchoPlanarPulseSequence: YES
bids:
<<: *fmap_dicoment_PEPolar
suffix: epi
meta: *fmap_meta
- provenance:
attributes: *fmap_dicomattr
bids:
<<: *fmap_dicoment_PEPolar
suffix: m0scan
meta: *fmap_meta
- provenance:
attributes: *fmap_dicomattr
bids: &fmap_dicoment_TB1DAM # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
flip:
inv:
part: ['', mag, phase, real, imag, 0]
run: <<>>
chunk:
suffix: TB1DAM
meta: &fmap_meta_B0Field
B0FieldIdentifier:
- provenance:
attributes: *fmap_dicomattr
bids: &fmap_dicoment_TB1EPI # See: schema/datatypes/fmap.yaml
acq: <<filepath:/.*/...(.*)/.*>>
ce:
rec:
flip:
echo:
inv:
part: ['', mag, phase, real, imag, 0]
run: <<>>
chunk:
suffix: TB1EPI
meta: *fmap_meta_B0Field
- provenance:
attributes: *fmap_dicomattr
bids: &fmap_dicoment_RFFieldMaps # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
flip:
echo:
inv:
part: ['', mag, phase, real, imag, 0]
run: <<>>
chunk:
suffix: TB1AFI
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*B1.?map.*
ImageType: .*FLIP ANGLE MAP.*
bids:
<<: *fmap_dicoment_RFFieldMaps # See: https://bids-specification.readthedocs.io/en/stable/99-appendices/11-qmri.html#tb1tfl-and-tb1rfm-specific-notes
acq: famp
suffix: TB1TFL
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*B1map.*
ImageType: .*'M'.*
bids:
<<: *fmap_dicoment_RFFieldMaps
acq: anat
suffix: TB1TFL
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*RF.?map.*
ImageType: .*'M'.*
bids:
<<: *fmap_dicoment_RFFieldMaps
acq: anat
suffix: TB1RFM
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*RF.?map.*
bids:
<<: *fmap_dicoment_RFFieldMaps
acq: famp
suffix: TB1RFM
meta: *fmap_meta_B0Field
- provenance:
attributes: *fmap_dicomattr
bids:
<<: *fmap_dicoment_RFFieldMaps
suffix: RB1COR
meta: *fmap_meta_B0Field
- provenance:
attributes: *fmap_dicomattr
bids: &fmap_dicoment_TB1SRGE # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
flip:
echo:
inv:
part: ['', mag, phase, real, imag, 0]
run: <<>>
chunk:
suffix: TB1SRGE
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*B1.?map.*
ImageType: .*FLIP ANGLE MAP.*
bids: &fmap_dicoment_parametric # See: schema/datatypes/fmap.yaml
acq: <filepath:/.*/...(.*)/.*/>
ce:
rec:
run: <<>>
chunk:
suffix: TB1map
meta: *fmap_meta_B0Field
- provenance:
attributes:
<<: *fmap_dicomattr
ProtocolName: (?i).*B1.?map.*
bids:
<<: *fmap_dicoment_parametric
suffix: RB1map
meta: *fmap_meta_B0Field
pet: # ----------------------- All PET runs ---------------------------
- provenance:
attributes: &pet_dicomattr
Modality: PT
StudyDescription:
SeriesDescription:
SeriesType:
Radiopharmaceutical:
ReconstructionMethod:
ImageType:
NumberOfSlices:
NumberOfTimeSlices:
SliceThickness:
PixelSpacing:
Rows:
Columns:
bids: &pet_dicoment_pet # See: schema/datatypes/pet.yaml
task: <filepath:/.*/...(.*)/.*/>
trc: <Radiopharmaceutical>
rec: ['', acdyn, acstat, nacdyn, nacstat, 0]
run: <<>>
suffix: pet
meta: &pet_meta
TracerName: <<Radiopharmaceutical>>
TracerRadionuclide:
InjectedRadioactivity: <<RadionuclideTotalDose>>
InjectedRadioactivityUnits:
InjectedMass:
InjectedMassUnits:
ModeOfAdministration:
SpecificRadioactivity:
SpecificRadioactivityUnits:
TimeZero: <<RadiopharmaceuticalStartTime>>
InjectionStart: <<ContrastBolusStartTime>>
FrameDuration: <<ActualFrameDuration>>
Units:
- provenance:
attributes: *pet_dicomattr
bids:
<<: *pet_dicoment_pet
suffix: events
meta: *pet_meta
- provenance:
attributes: *pet_dicomattr
bids:
<<: *pet_dicoment_pet
recording:
suffix: blood
meta: *pet_meta
eeg: # ----------------------- All EEG data ---------------------------
- provenance:
attributes:
Modality: EEG
ProtocolName:
SeriesDescription:
bids: # See: schema/datatypes/eeg.yaml
acq: <ProtocolName>
task: <SeriesDescription>
run: <<>>
suffix: eeg
ieeg: # ----------------------- All iEEG data --------------------------
- provenance:
attributes: