.. _scil_tractogram_extract_ushape:

scil_tractogram_extract_ushape
==============================

::

	usage: __main__.py [-h] [--minU MINU] [--maxU MAXU]
	                   [--remaining_tractogram filename] [--no_empty]
	                   [--display_counts] [--indent INDENT] [--sort_keys]
	                   [--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_tractogram out_tractogram
	
	This script extracts streamlines depending on their U-shapeness.
	This script is a replica of Trackvis method.
	
	When ufactor is close to:
	*  0 it defines straight streamlines
	*  1 it defines U-fibers
	* -1 it defines S-fibers
	
	positional arguments:
	  in_tractogram         Tractogram input file name.
	  out_tractogram        Output tractogram file name.
	
	options:
	  -h, --help            show this help message and exit
	  --minU MINU           Min ufactor value. [0.5]
	  --maxU MAXU           Max ufactor value. [1.0]
	  --remaining_tractogram filename
	                        If set, saves remaining streamlines.
	  --no_empty            Do not write file if there is no streamline.
	  --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