.. _scil_bundle_reject_outliers:

scil_bundle_reject_outliers
===========================

::

	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