cortex.freesurfer.import_subj(fs_subject, cx_subject=None, freesurfer_subject_dir=None, whitematter_surf='smoothwm')[source]

Imports a subject from freesurfer

This will overwrite (after giving a warning and an option to continue) the pre-existing subject, including all blender cuts, masks, transforms, etc., and re-generate surface info files (curvature, sulcal depth, thickness) stored in the surfinfo/ folder for the subject. All cached files for the subject will be deleted.


Freesurfer subject name

cx_subjectstring, optional

Pycortex subject name (These variable names should be changed). By default uses the same name as the freesurfer subject. Best to stick to that convention, if possible (your life will go more smoothly.) This optional kwarg is for edge cases.

freesurfer_subject_dirstring, optional

Freesurfer subject directory to pull data from. By default uses the directory given by the environment variable $SUBJECTS_DIR.

whitematter_surfstring, optional

Which whitematter surface to import as ‘wm’. By default uses ‘smoothwm’, but that surface is smoothed and may not be appropriate. A good alternative is ‘white’.