cortex.segment.init_subject

cortex.segment.init_subject(subject, filenames, do_import_subject=False, **kwargs)

Run the first initial segmentation for a subject’s anatomy (in Freesurfer).

This function creates a Freesurfer subject and runs autorecon-all, then (optionally) imports the subject into the pycortex database.

NOTE: This function requires a functional Freesurfer install! Also, still can’t handle T2 weighted anatomical volume input. Please use Freesurfer directly (and then import) for advanced recon-all input options; this is just a convenience function.

Parameters:

subjectstr

The name of the subject (this subject is created in the Freesurfer SUBJECTS_DIR)

filenamesstr or list

Freesurfer-compatible filename(s) for the anatomical image(s). This can be the first dicom file of a series of dicoms, a nifti file, an mgz file, etc.

do_import_subjectbool

Whether to import the Freesurfer-processed subject (without further) editing) into pycortex. False by default, since we recommend editing (or at least inspecting) the brain mask and white matter segmentations prior to importing into pycortex.

**kwargs

Additional keyword arguments are forwarded to cortex.freesurfer.autorecon. useful ones: parallel=True, n_cores=4 (or more, if you have them)