Add Freesurfer labels from different subjects in the average mesh (fsaverage).

freesurfer_label_operations.py

"""Add freesurfer labels similar to 'fslmaths -add'.

Use an .mgh file to read relevant information such as headers or number of
vertices.

Note: Freesurfer operations can be performed on .mgh format without
getting unrecognized data type error.
"""

import numpy as np
from nibabel import save
from nibabel import freesurfer as fs

# path of the output file
outfile = '/path/to/your/subject/label_operations/lh.file'

# mgh format is more useful, freesurfer operations can be on on this file
mgh = fs.mghformat.load(
    '/path/to/your/subject/fsaverage/surf/lh.orig.avg.area.mgh')

# names of the rois
names = ['/path/to/your/subject_1/file_lh_roi.label',
         '/path/to/your/subject_2/file_lh_roi.label',
         '/path/to/your/subject_3/file_lh_roi.label',
         '/path/to/your/subject_4/file_lh_roi.label']

# one example statistical surface file to get the number of vertices
surf_map = mgh.get_data()
surf_map = surf_map * 0  # start with all zeros

for i in range(len(names)):
    temp = np.zeros(surf_map.size)
    i_roi = fs.read_label(names[i])
    temp[i_roi] = 1
    surf_map[:, 0, 0] = surf_map[:, 0, 0] + temp

# save as mgh
out = fs.MGHImage(surf_map, mgh.affine, mgh.header)
save(out, outfile + '.mgh')