xcp_d.utils.bids

Utilities for fmriprep bids derivatives and layout.

Most of the code is copied from niworkflows. A PR will be submitted to niworkflows at some point.

Functions

collect_data(bids_dir, input_type, ...[, ...])	Collect data from a BIDS dataset.
collect_participants(bids_dir[, ...])	Collect a list of participants from a BIDS dataset.
collect_run_data(layout, input_type, ...)	Collect data associated with a given BOLD file.
collect_surface_data(layout, participant_label)	Collect surface files from preprocessed derivatives.
get_entity(filename, entity)	Extract a given entity from a BIDS filename via string manipulation.
get_freesurfer_dir(fmri_dir)	Find FreeSurfer derivatives associated with preprocessing pipeline.
get_freesurfer_sphere(freesurfer_path, ...)	Find FreeSurfer sphere file.
get_preproc_pipeline_info(input_type, fmri_dir)	Get preprocessing pipeline information from the dataset_description.json file.
group_across_runs(in_files)	Group preprocessed BOLD files by unique sets of entities, ignoring run.
write_dataset_description(fmri_dir, xcpd_dir)	Write dataset_description.json file for derivatives.

Exceptions

BIDSError(message, bids_root)	A generic error related to BIDS datasets.
BIDSWarning	A generic warning related to BIDS datasets.