freesurfer gifti transformation to native space

fs_gifti_xfm.py

#DOES NOT WORK: GIFTI READ/WRITE is broken
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=np.float32)

# 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

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

# set the data
surf.darrays[0] = da.from_array(xfmda0.astype(indtype), da.intent, da.datatype)
surf.darrays[1] = da.from_array(xfmda1.astype(indtype), da.intent, da.datatype)

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

fs_to_native_vtk.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=np.float32)

# 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

# write directly to vtk
from tvtk.api import tvtk
mesh = tvtk.PolyData(points=xfmda0, polys=surf.darrays[1].data)
w = tvtk.XMLPolyDataWriter(input=mesh, file_name='polydata.vtp')
w.write()