freesurfer gifti transformation to native space

fs_gifti_xfm.py

import nibabel as nb
import nibabel.gifti as gifti

# load combined file
# created with: mris_convert --combinesurfs lh.pial rh.pial ./pial.gii
surf = gifti.read('pial.gii')

#load orig affine transform
ao = nb.load('orig.nii').get_affine()

# load conformed affine
ac = nb.load('conformed.nii').get_affine()

# create freesurfer conformed volume to surface transform matrix
import numpy as np
M = np.array([[-1,0,0,128],
              [0, 0, 1, -128],
              [0, -1, 0, 128],
              [0,0,0,1]],dtype=float)

# create transform to go to native space
xfm = np.dot(ac, np.linalg.inv(M))

# transform the two data arrays storing left and right vertices
xfmda0 = np.dot(xfm, np.hstack((surf.darrays[0].data, np.ones((surf.darrays[0].data.shape[0],1)))).T)[:3,:].T
xfmda1 = np.dot(xfm, np.hstack((surf.darrays[1].data, np.ones((surf.darrays[1].data.shape[0],1)))).T)[:3,:].T

indtype = surf.darrays[0].data.dtype

# set the data
surf.darrays[0].data = xfmda0.astype(indtype)
surf.darrays[1].data = xfmda1.astype(indtype)

# write to file
gifti.write(surf, 'xfmpial.gii')