Using Annotation FilesΒΆ

Display a Freesurfer cortical parcellation from an annotation file.


Python source code:

import os
from os.path import join as pjoin
from surfer import Brain


subject_id = 'fsaverage'
hemi = 'both'
surface = 'inflated'
view = 'frontal'

Bring up the visualization
brain = Brain(subject_id, hemi, surface, views=view,
              cortex="bone", background="ivory")

Display the 'aparc' parcellation borders.
To use annotations that live in your subject's
label directory, just use the annot name.

You can also display the regions with "filled in" colors
brain.add_annotation("aparc", borders=False)

You may also provide a full path to an annotation file
at an arbitray location on the disc. You can also
plot things separately for the left and right hemispheres.
subjects_dir = os.environ["SUBJECTS_DIR"]
annot_path = pjoin(subjects_dir, subject_id, "label", "lh.aparc.annot")
brain.add_annotation(annot_path, hemi='lh', borders=False, alpha=.75)
annot_path = pjoin(subjects_dir, subject_id, "label", "rh.aparc.a2009s.annot")
brain.add_annotation(annot_path, hemi='rh', borders=2, remove_existing=False)