netneurotools.freesurfer.apply_prob_atlas

netneurotools.freesurfer.apply_prob_atlas(subject_id, gcs, hemi, *, orig='white', annot=None, ctab=None, subjects_dir=None, use_cache=True, quiet=False)[source]

Create an annotation file for subject_id by applying atlas in gcs.

Runs subprocess calling FreeSurfer’s “mris_ca_label” function; as such, FreeSurfer must be installed and accesible on the local system path.

Parameters:

  • subject_id (str) – FreeSurfer subject ID

  • gcs (str) – Filepath to .gcs file containing classifier array

  • hemi ({'lh', 'rh'}) – Hemisphere corresponding to gcs file

  • orig (str, optional) – Original surface to which to apply classifer. Default: ‘white’

  • annot (str, optional) – Path to output annotation file to generate. If set to None, the name is created from the provided hemi and gcs. If provided as a relative path, it is assumed to stem from subjects_dir/subject_id. Default: None

  • ctab (str, optional) – Path to colortable corresponding to gcs. Default: None

  • subjects_dir (str, optional) – Path to FreeSurfer subject directory. If not set, will inherit from the environmental variable $SUBJECTS_DIR. Default: None

  • use_cache (bool, optional) – Whether to check for existence of annot in directory specified by `{subjects_dir}/{subject_id}/label’ and use that, if it exists. If False, will create a new annot file. Default: True

  • quiet (bool, optional) – Whether to restrict status messages. Default: False

Returns:

annot – Path to generated annotation file

Return type:

str