.. _scil_viz_tractogram_collisions:

scil_viz_tractogram_collisions
==============================

::

	usage: __main__.py [-h] [--in_tractogram_obstacle IN_TRACTOGRAM_OBSTACLE]
	                   [--ref_tractogram REF_TRACTOGRAM]
	                   [--out_screenshot OUT_SCREENSHOT]
	                   [--win_size WIN_SIZE WIN_SIZE] [-f] [--reference REFERENCE]
	                   in_tractogram_invalid
	
	Visualize collisions given by scil_tractogram_filter_collisions with
	the --save_colliding parameter.
	
	positional arguments:
	  in_tractogram_invalid
	                        Tractogram file containing the colliding 
	                        streamlines that have been filtered, along their 
	                        collision point as data_per_streamline (must be 
	                        .trk). This file is obtained from the 
	                        scil_tractogram_filter_collisions script.
	
	options:
	  -h, --help            show this help message and exit
	  --in_tractogram_obstacle IN_TRACTOGRAM_OBSTACLE
	                        Tractogram file containing the streamlines that 
	                        that [in_tractogram_invalid] has collided with. Will 
	                        be overlaid in the viewing window. This file is 
	                        obtained from the scil_tractogram_filter_collisions 
	                        script.
	  --ref_tractogram REF_TRACTOGRAM
	                        Tractogram file containing the full tractogram 
	                        as visual reference (must be .trk or .tck). It will be 
	                        overlaid in white and very low opacity.
	  --out_screenshot OUT_SCREENSHOT
	                        If set, save a screenshot of the result in the 
	                        specified filename (.png, .bmp, .jpeg or .jpg).
	  --win_size WIN_SIZE WIN_SIZE
	  -f                    Force overwriting of the output files.
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	
	2.2.2