def mrtrix_tck_to_trk():
ref_img = nib.load(output_dir + "/bundle_segmentations" + dir_postfix + "/" + bundle + ".nii.gz")
reference_affine = ref_img.affine
reference_shape = ref_img.get_data().shape[:3]
fiber_utils.convert_tck_to_trk(output_dir + "/" + tracking_folder + "/" + bundle + ".tck",
output_dir + "/" + tracking_folder + "/" + bundle + ".trk",
reference_affine, reference_shape, compress_err_thr=0.1, smooth=None,
nr_cpus=nr_cpus, tracking_format=output_format)
subprocess.call("rm -f " + output_dir + "/" + tracking_folder + "/" + bundle + ".tck", shell=True)
def _mrtrix_tck_to_trk(output_dir, tracking_folder, dir_postfix, bundle,
output_format, nr_cpus):
ref_img = nib.load(output_dir + "/bundle_segmentations" + dir_postfix +
"/" + bundle + ".nii.gz")
reference_affine = ref_img.affine
# Don't need to load all the data to get its shape / dimmensions, info is stored in the image header
# reference_shape = ref_img.get_data().shape[:3]
reference_shape = ref_img.header.get_data_shape()[:3]
fiber_utils.convert_tck_to_trk(
output_dir + "/" + tracking_folder + "/" + bundle + ".tck",
output_dir + "/" + tracking_folder + "/" + bundle + ".trk",
reference_affine,
reference_shape,
compress_err_thr=0.1,
smooth=None,
nr_cpus=nr_cpus,
tracking_format=output_format)
subprocess.call("rm -f " + output_dir + "/" + tracking_folder + "/" +
bundle + ".tck",
shell=True)