.. _scil_tractogram_detect_loops:

scil_tractogram_detect_loops
============================

::

	usage: __main__.py [-h] [--looping_tractogram out_filename] [--qb [threshold]]
	                   [--angle ANGLE] [--display_counts] [--no_empty]
	                   [--indent INDENT] [--sort_keys] [--processes NBR]
	                   [--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_tractogram out_tractogram
	
	This script can be used to remove loops in two types of streamline datasets:
	
	  - Whole brain: For this type, the script removes streamlines if they
	    make a loop with an angle of more than 360 degrees. It's possible to change
	    this angle with the --angle option. Warning: Don't use --qb option for a
	    whole brain tractography.
	
	  - Bundle dataset: For this type, it is possible to remove loops and
	    streamlines outside the bundle. For the sharp angle turn, use --qb option.
	
	See also:
	    scil_tractogram_filter_by_anatomy
	
	------------------------------------------------------------------------------
	Reference:
	[1] QuickBundles, based on [Garyfallidis12] Frontiers in Neuroscience, 2012.
	------------------------------------------------------------------------------
	
	positional arguments:
	  in_tractogram         Tractogram input file name.
	  out_tractogram        Output tractogram without loops.
	
	options:
	  -h, --help            show this help message and exit
	  --looping_tractogram out_filename
	                        If set, saves detected looping streamlines.
	  --qb [threshold]      If set, uses QuickBundles to detect outliers (loops, sharp angle 
	                        turns). Given threshold is the maximal streamline to bundle 
	                        distance for a streamline to be considered as a tracking error.
	                        Default if set: [8.0]
	  --angle ANGLE         Maximum looping (or turning) angle of
	                        a streamline in degrees. [360]
	  --display_counts      Print streamline count before and after filtering
	  --no_empty            If set, will not save outputs if they are empty.
	  --processes NBR       Number of sub-processes to start. 
	                        Default: [1]
	  --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