usage: __main__.py [-h] [--cut_invalid] [--remove_single_point]
[--remove_overlapping_points] [--threshold THRESHOLD]
[--no_empty] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_tractogram out_tractogram
Removal of streamlines that are out of the volume bounding box. In voxel space
no negative coordinate and no above volume dimension coordinate are possible.
Any streamline that do not respect these two conditions are removed.
The --cut_invalid option will cut streamlines so that their longest segment are
within the bounding box
Formerly: scil_remove_invalid_streamlines.py
positional arguments:
in_tractogram Tractogram filename. Format must be one of
trk, tck, vtk, fib, dpy.
out_tractogram Output filename. Format must be one of
trk, tck, vtk, fib, dpy.
options:
-h, --help show this help message and exit
--cut_invalid Cut invalid streamlines rather than removing them.
Keep the longest segment only.
--remove_single_point
Consider single point streamlines invalid.
--remove_overlapping_points
Consider streamlines with overlapping points invalid.
--threshold THRESHOLD
Maximum distance between two points to be considered overlapping [0.001 mm].
--no_empty Do not save empty tractogram.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.