Visualization of brain regions after FreeSurfer parcellation

parcellation_visualization.py

from __future__ import print_function

import os
import numpy as np

from surfer import Brain
from mayavi import mlab
import nibabel as nib

subjects_folder = os.environ["SUBJECTS_DIR"]
subject_id      = 'fsaverage'
hemi            = "both"
surf            = "smoothwm"
parcel_method   = 'aparc.annot'

brain = Brain(subject_id, hemi, surf)

if hemi != 'both':
    aparc_filename = os.path.join(subjects_folder, subject_id, 'label', '.'.join([hemi,parcel_method]))
    labels, ctab, names = nib.freesurfer.read_annot(aparc_filename)
else:
    aparc_fn_lh = os.path.join(subjects_folder, subject_id, 'label', '.'.join(['lh',parcel_method]))
    aparc_fn_rh = os.path.join(subjects_folder, subject_id, 'label', '.'.join(['rh',parcel_method]))
    labels_lh, ctab_lh, names_lh = nib.freesurfer.read_annot(aparc_fn_lh)
    labels_rh, ctab_rh, names_rh = nib.freesurfer.read_annot(aparc_fn_rh)
    assert names_lh == names_rh, 'rh not eq lh'
    names = names_lh

print('Parcellation regions:')
for i in names:
    print(i)

reg_name = raw_input('If you want to select parcellation region, specify its name here:')

if not reg_name in names:
    vals = np.arange(0,1,1./len(names))
else:
    vals = np.zeros(len(names)) - 1
    vals[names.index(reg_name)] = 1

if hemi != 'both':
    vtx = vals[labels]
    vtx[labels==-1] = -1
    brain.add_data(vtx, 0, 1, thresh=0, colormap='jet', alpha=0.8)
else:
    vtx_lh = vals[labels_lh]
    vtx_rh = vals[labels_rh]
    vtx_lh[labels_lh == -1] = -1
    vtx_rh[labels_rh == -1] = -1
    #import pdb; pdb.set_trace()
    brain.add_data(vtx_lh, 0, 1, thresh=0, colormap='jet', alpha=0.8, hemi='lh')
    brain.add_data(vtx_rh, 0, 1, thresh=0, colormap='jet', alpha=0.8, hemi='rh')
mlab.show()