cmtklib.bids.utils module
This module provides CMTK Utility functions to handle BIDS datasets.
CreateBIDSStandardParcellationLabelIndexMappingFile
Bases: nipype.interfaces.base.core.BaseInterface
Creates the BIDS standard generic label-index mapping file that describes parcellation nodes.
- roi_colorluta pathlike object or string representing an existing file
Path to FreesurferColorLUT.txt file that describes the RGB color of the graph nodes for a given parcellation.
- roi_graphmla pathlike object or string representing an existing file
Path to graphml file that describes graph nodes for a given parcellation.
- verbosea boolean
Verbose mode.
- roi_bids_tsva pathlike object or string representing a file
Output BIDS standard generic label-index mapping file that describes parcellation nodes.
CreateCMPParcellationNodeDescriptionFilesFromBIDSFile
Bases: nipype.interfaces.base.core.BaseInterface
Creates CMP graphml and FreeSurfer colorLUT files that describe parcellation nodes from the BIDS TSV file
- roi_bids_tsva pathlike object or string representing an existing file
Output BIDS standard generic label-index mapping file that describes parcellation nodes.
- roi_colorluta pathlike object or string representing a file
Path to FreesurferColorLUT.txt file that describes the RGB color of the graph nodes for a given parcellation.
- roi_graphmla pathlike object or string representing a file
Path to graphml file that describes graph nodes for a given parcellation.
CreateMultipleCMPParcellationNodeDescriptionFilesFromBIDSFile
Bases: nipype.interfaces.base.core.BaseInterface
Creates CMP graphml and FreeSurfer colorLUT files describing parcellation nodes from a list of BIDS TSV files
roi_bids_tsvs : a list of items which are a pathlike object or string representing an existing file
roi_colorluts : a list of items which are a pathlike object or string representing a file roi_graphmls : a list of items which are a pathlike object or string representing a file
- cmtklib.bids.utils.get_native_space_files(filepathlist)[source]
Return a list of files without
_space-<label>_
in the filename.
- cmtklib.bids.utils.get_native_space_no_desc_files(filepathlist)[source]
Return a list of files without
_space-<label>_
and_desc-<label>_
in the filename.
- cmtklib.bids.utils.get_native_space_tsv_sidecar_files(filepathlist)[source]
Return path to tsv sidecar file of a list of niftis (
nii.gz
) without_space-<label>_
in their filename.
- cmtklib.bids.utils.write_derivative_description(bids_dir, deriv_dir, pipeline_name)[source]
Write a dataset_description.json in each type of CMP derivatives.
- Parameters
bids_dir (string) – BIDS root directory
deriv_dir (string) – Output/derivatives directory
pipeline_name (string) – Type of derivatives (
['cmp-<version>', 'freesurfer-<version>', 'nipype-<version>']
)