cortex.freesurfer.import_subj

cortex.freesurfer.import_subj(freesurfer_subject, pycortex_subject=None, freesurfer_subject_dir=None, whitematter_surf='smoothwm')

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.

Parameters:

freesurfer_subjectstr

Freesurfer subject name

pycortex_subjectstr, optional

Pycortex subject name. By default it uses the freesurfer subject name. It is advised to stick to that convention, if possible (your life will go more smoothly.)

freesurfer_subject_dirstr, optional

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

whitematter_surfstr, 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’.

Notes

This function uses command line functions from freesurfer, so you should make sure to have freesurfer sourced before running this function.

This function will also generate the fiducial surfaces for the subject, which are halfway between the white matter and pial surfaces. The surfaces will be stored in the freesurfer subject’s directory. These fiducial surfaces are used for cutting and flattening.