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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script is made to fix DSI-Studio TRK file (unknown space/convention) to
make it compatible with TrackVis, MI-Brain, Dipy Horizon (Stateful Tractogram).
The script either make it match with an anatomy from DSI-Studio.
This script was tested on various datasets and worked on all of them. However,
always verify the results and if a specific case does not work. Open an issue
on the Scilpy GitHub repository.
WARNING: This script is still experimental, DSI-Studio evolves quickly and
results may vary depending on the data itself as well as DSI-studio version.
"""
import argparse
import os
from trx.workflows import convert_dsi_studio
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_dsi_tractogram', metavar='IN_DSI_TRACTOGRAM',
help='Path of the input tractogram file from DSI studio '
'(.trk).')
p.add_argument('in_dsi_fa', metavar='IN_DSI_FA',
help='Path of the input FA from DSI Studio (.nii.gz).')
p.add_argument('out_tractogram', metavar='OUT_TRACTOGRAM',
help='Path of the output tractogram file.')
invalid = p.add_mutually_exclusive_group()
invalid.add_argument('--remove_invalid', action='store_true',
help='Remove the streamlines landing out of the '
'bounding box.')
invalid.add_argument('--keep_invalid', action='store_true',
help='Keep the streamlines landing out of the '
'bounding box.')
p.add_argument('-f', dest='overwrite', action='store_true',
help='Force overwriting of the output files.')
return p
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if os.path.isfile(args.out_tractogram) and not args.overwrite:
raise IOError('{} already exists, use -f to overwrite.'.format(
args.out_tractogram))
convert_dsi_studio(args.in_dsi_tractogram, args.in_dsi_fa,
args.out_tractogram, remove_invalid=args.remove_invalid,
keep_invalid=args.keep_invalid)
if __name__ == "__main__":
main()
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