cortex.freesurfer.autorecon

cortex.freesurfer.autorecon(fs_subject, type='all', parallel=True, n_cores=None)

Run Freesurfer’s autorecon-all command for a given freesurfer subject

Parameters:

fs_subjectstring

Freesurfer subject ID (should be a folder in your freesurfer $SUBJECTS_DIR)

typestring

Which steps of autorecon-all to perform. {‘all’, ‘1’,’2’,’3’,’cp’,’wm’, ‘pia’}

parallelbool

Whether to parallelize the recon. Only has an effect for the ‘2’, ‘wm’, and ‘all’ steps, which are the only ones freesurfer can parallelize.

n_coresint

Number of cores to use when parallel is True. None (default) uses all available cores.