usage: __main__.py [-h] [--remaining_bundle REMAINING_BUNDLE] [--alpha ALPHA]
[--display_counts] [--indent INDENT] [--sort_keys]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
[-f]
in_bundle out_bundle
Clean a bundle (inliers/outliers) using hiearchical clustering.
http://archive.ismrm.org/2015/2844.html
If spurious streamlines are dense, it is possible they will not be recognized
as outliers. Manual cleaning may be required to overcome this limitation.
positional arguments:
in_bundle Fiber bundle file to remove outliers from.
out_bundle Fiber bundle without outliers.
options:
-h, --help show this help message and exit
--remaining_bundle REMAINING_BUNDLE
Removed outliers.
--alpha ALPHA Percent of the length of the tree that clusters of individual streamlines will be pruned. [0.6]
--display_counts Print streamline count before and after filtering
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING,ERROR}]
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.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
2.2.2