qsiprep.utils.bids module

Utilities to handle BIDS inputs

Fetch some test data

>>> import os
>>> from niworkflows import data
>>> data_root = data.get_bids_examples(variant='BIDS-examples-1-enh-ds054')
>>> os.chdir(data_root)

exception qsiprep.utils.bids.BIDSError(message, bids_root)

Bases: ValueError

exception qsiprep.utils.bids.BIDSWarning

Bases: RuntimeWarning

qsiprep.utils.bids.collect_data(bids_dir, participant_label, filters=None, bids_validate=True)

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

qsiprep.utils.bids.collect_participants(bids_dir, participant_label=None, strict=False, bids_validate=True)

List the participants under the BIDS root and checks that participants designated with the participant_label argument exist in that folder.

Returns the list of participants to be finally processed.

Requesting all subjects in a BIDS directory root:

>>> collect_participants('ds114')
['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']

Requesting two subjects, given their IDs:

>>> collect_participants('ds114', participant_label=['02', '04'])
['02', '04']

Requesting two subjects, given their IDs (works with ‘sub-’ prefixes):

>>> collect_participants('ds114', participant_label=['sub-02', 'sub-04'])
['02', '04']

Requesting two subjects, but one does not exist:

>>> collect_participants('ds114', participant_label=['02', '14'])
['02']

>>> collect_participants('ds114', participant_label=['02', '14'],
...                      strict=True)  
Traceback (most recent call last):
qsiprep.utils.bids.BIDSError:
...

qsiprep.utils.bids.update_metadata_from_nifti_header(metadata, nifti_file)

Update a BIDS metadata dictionary with info from a NIfTI header.

Code borrowed from CuBIDS.

qsiprep.utils.bids.validate_input_dir(exec_env, bids_dir, participant_label)

qsiprep.utils.bids.write_bidsignore(deriv_dir)

qsiprep.utils.bids.write_derivative_description(bids_dir, deriv_dir)