trackvis.py

import numpy as np
from nibabel import load
import nibabel.trackvis as nibtrk

# filename = "DeterministicTractography/QBALLRecon/hardiO10.trk"

trkfilename = "/software/data/STUT/DTI_TV/PWS04/dtk_35/dti_35.trk" #%hardiO10.trk_cross_streamline_id_20.trk"
trkfilename_out = "newtracks.trk"
bfilename =  "/software/data/STUT/DTI_TV/PWS04/dt_recon/lowb.nii"
mrfilename =  "/software/data/MIBR/data/PWS04/head.nii"

reg = np.genfromtxt('/software/data/STUT/DTI_TV/PWS04/dt_recon/register.dat',skiprows=4,comments='r')

bimg = load(bfilename)
mrimg = load(mrfilename)
M = np.array([[-1,0,0,128],
              [0, 0, 1, -128],
              [0, -1, 0, 128],
              [0,0,0,1]],dtype=float)
M1 = np.array([[-2,0,0,128],
              [0, 0, 2, -64],
              [0, -2, 0, 128],
              [0,0,0,1]],dtype=float)

s = nibtrk.read(trkfilename)
tracks = s[0]
hdr = s[1]

aff = bimg.get_affine()
#xfm = np.dot(np.dot(np.dot(img2.get_affine(),np.linalg.inv(M)),reg),aff)
xfm = np.dot(mrimg.get_affine(),np.dot(np.linalg.inv(M),np.dot(np.linalg.inv(reg),M1)))

print xfm

A = np.dot(aff[0:3,0:3],np.diag(1./hdr['voxel_size']))
b = aff[0:3,3]


for t in xrange( len( tracks ) ):

  track = tracks[t]

  xyz = track[0]
  new_xyz = (np.dot(A, xyz.T) + b[:,None]).transpose()

  newTrack = ( new_xyz, track[1], track[2] )

  # replace the old track with the newTrack
  tracks[t] = newTrack

# save the warped tracks
nibtrk.write( trkfilename_out, tracks, hdr, points_space='voxel' )

@satra I modified your code to use nibabel instead of streamlines.py but alas it does not give good results for me. the old version with streamlines.py did not work at all (I think due to the newer trackvis format - streamlines.py is very old).