dmriprep.utils.bids module

Utilities to handle BIDS inputs.

dmriprep.utils.bids.collect_derivatives(derivatives_dir, entities, fieldmap_id=None, spec=None, patterns=None)View on GitHub

Gather existing derivatives and compose a cache.

dmriprep.utils.bids.extract_entities(file_list)View on GitHub

Return a dictionary of common entities given a list of files.

Examples

>>> extract_entities("sub-01/anat/sub-01_T1w.nii.gz")
{'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': '.nii.gz'}
>>> extract_entities(["sub-01/anat/sub-01_T1w.nii.gz"] * 2)
{'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': '.nii.gz'}
>>> extract_entities(["sub-01/anat/sub-01_run-1_T1w.nii.gz",
...                   "sub-01/anat/sub-01_run-2_T1w.nii.gz"])
{'subject': '01', 'run': [1, 2], 'suffix': 'T1w', 'datatype': 'anat', 'extension': '.nii.gz'}

dmriprep.utils.bids.validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True)View on GitHub

dmriprep.utils.bids.write_bidsignore(deriv_dir, bids_ignore={'*.html', '*.surf.gii', '*_dwiref.nii.gz', '*_xfm.*', 'figures/', 'logs/'})View on GitHub

dmriprep.utils.bids.write_derivative_description(bids_dir, deriv_dir)View on GitHub