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Script that converts TCK to TRK using https://github.com/MarcCote/nibabel/tree/streamlines_tck
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import os | |
import argparse | |
import nibabel as nib | |
from nibabel.streamlines import Field | |
from nibabel.orientations import aff2axcodes | |
def build_argparser(): | |
DESCRIPTION = "Convert tractograms (TCK -> TRK)." | |
p = argparse.ArgumentParser(description=DESCRIPTION) | |
p.add_argument('anatomy', help='reference anatomy (.nii|.nii.gz.') | |
p.add_argument('tractograms', metavar='tractogram', nargs="+", help='list of tractograms (.tck).') | |
p.add_argument('-f', '--force', action="store_true", help='overwrite existing output files.') | |
return p | |
def main(): | |
parser = build_argparser() | |
args = parser.parse_args() | |
try: | |
nii = nib.load(args.anatomy) | |
except: | |
parser.error("Expecting anatomy image as first agument.") | |
for tractogram in args.tractograms: | |
if nib.streamlines.detect_format(tractogram) is not nib.streamlines.TckFile: | |
print("Skipping non TCK file: '{}'".format(tractogram)) | |
continue | |
output_filename = tractogram[:-4] + '.trk' | |
if os.path.isfile(output_filename) and not args.force: | |
print("Skipping existing file: '{}'. Use -f to overwrite.".format(output_filename)) | |
continue | |
header = {} | |
header[Field.VOXEL_TO_RASMM] = nii.affine.copy() | |
header[Field.VOXEL_SIZES] = nii.header.get_zooms()[:3] | |
header[Field.DIMENSIONS] = nii.shape[:3] | |
header[Field.VOXEL_ORDER] = "".join(aff2axcodes(nii.affine)) | |
tck = nib.streamlines.load(tractogram) | |
nib.streamlines.save(tck.tractogram, output_filename, header=header) | |
if __name__ == '__main__': | |
main() |
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