.. _scil_tractogram_qbx:

scil_tractogram_qbx
===================

::

	usage: __main__.py [-h] [--nb_points NB_POINTS]
	                   [--out_centroids OUT_CENTROIDS] [--reference REFERENCE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_tractogram dist_thresh out_clusters_dir
	
	Compute clusters using QuickBundlesX and save them separately.
	We cannot know the number of clusters in advance.
	
	----------------------------------------------------------------------------------
	References Quickbundles[1] QuickbundlesX [2] :
	
	[1] Garyfallidis, E. et al. (2012). Quickbundles, a method for tractography
	simplification. Frontiers in neuroscience, 6, 175.
	
	[2] Garyfallidis, E. et al. (2016) QuickBundlesX: sequential clustering of millions
	of streamlines in multiple levels of detail at record execution time. 24th
	International Society of Magnetic Resonance in Medicine (ISMRM).
	
	"QuickBundlesX shows a remarkable 20+X speedup over its predecessor"
	----------------------------------------------------------------------------------
	
	positional arguments:
	  in_tractogram         Tractogram filename.
	                        Path of the input tractogram or bundle.
	  dist_thresh           Last QuickBundlesX threshold in mm. Typically 
	                        the value are between 10-20mm.
	  out_clusters_dir      Path where to save the clusters directory.
	
	options:
	  -h, --help            show this help message and exit
	  --nb_points NB_POINTS
	                        Streamlines will be resampled to have this number of points [20].
	  --out_centroids OUT_CENTROIDS
	                        Output tractogram filename.
	                        Format must be readable by the Nibabel API.
	  --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.
	
	2.2.2