.. _scil_bundle_explore_bundleseg:

scil_bundle_explore_bundleseg
=============================

::

	usage: __main__.py [-h] [--mask MASK] [--apply_config JSON] [-f]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_folder in_ref_img out_dir
	
	BundleSeg output visualization tool.
	
	This script allows visualization of segmented bundles and after-the-fact
	filtering to explore optimal thresholds for each bundle. It uses
	FURY for 3D rendering.
	It includes tools to slice images, filter streamlines, and interactively
	visualize bundles and a reference image.
	
	This script is intended to be used after running BundleSeg:
	    scil_tractogram_segment_with_bundleseg
	To explore thresholds the option --exploration_mode must be used to segment
	using a much higher distance threshold.
	
	positional arguments:
	  in_folder             Folder generated by BundleSeg containing the results.
	  in_ref_img            Background reference image.
	  out_dir               Output directory for filtered bundles.
	
	options:
	  -h, --help            show this help message and exit
	  --mask MASK           Binary mask used to render surfaces (VOI).
	  --apply_config JSON   Apply a configuration file to automatically filter.
	  -f                    Force overwriting of the output files.
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.