Rotate bvecs with ANTS transform matrix

rot_bvecs_ants.py

from scipy.io import loadmat
import numpy as np
import sys

if __name__ == "__main__":
	print('input_ants_rigid_transform input_bvecs output_bvec')

	# Loading Ants transform
	trans = loadmat(sys.argv[1])
	matrice = trans['AffineTransform_double_3_3'][:9].reshape((3,3))

	#loading bvecs
	bvecs = np.genfromtxt(sys.argv[2])
	# heuristic to have bvecs shape 3xN
	if bvecs.shape[0] != 3:
		bvecs = bvecs.T

	# Rotating bvecs
	newbvecs = np.dot(matrice, bvecs)

	# saving bvecs
	np.savetxt(sys.argv[3], newbvecs)

ex ants command:
antsRegistration -d 3 -o [./b0_28_to_16_,./b0_28_to_16_warped.nii.gz] -n BSpline -w [0.005,0.995] -u -r [b0_16_9.nii.gz,b0_28_7.nii.gz,1] -t Rigid[0.1] -m MI[b0_16_9.nii.gz,b0_28_7.nii.gz,1,32,Regular,0.25] -c [1000x500x250x100,1e-6,10] -f 8x4x2x1 -s 3x2x1x0vox