aslprep.utils.bids module

Utilities to handle BIDS inputs.

collect_anat_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patterns=None, session_id=None)

Gather existing derivatives and compose a cache.

collect_derivatives(derivatives_dir: Path, entities: dict, fieldmap_id: str | None = None, spec: dict | None = None, patterns: list[str] | None = None)

Gather existing derivatives and compose a cache.

collect_run_data(layout, asl_file)

Use pybids to retrieve the input data for a given participant.

find_atlas_entities(filename)

Extract atlas entities from filename.

get_entity(filename, entity)

Extract a given entity from a BIDS filename via string manipulation.

Parameters:

• filename (str) – Path to the BIDS file.

• entity (str) – The entity to extract from the filename.

Returns:

entity_value – The BOLD file’s entity value associated with the requested entity.

Return type:

str or None

write_atlas_dataset_description(atlas_dir)

Write dataset_description.json file for Atlas derivatives.

Parameters:

atlas_dir (str) – Path to the output XCP-D Atlases dataset.

write_bidsignore(deriv_dir)

Write .bidsignore file.

write_derivative_description(bids_dir, deriv_dir)

Write derivative dataset_description file.