.. _scil_bundle_pairwise_comparison:

scil_bundle_pairwise_comparison
===============================

::

	usage: __main__.py [-h] [--streamline_dice] [--ignore_zeros_in_BA]
	                   [--disable_streamline_distance]
	                   [--single_compare SINGLE_COMPARE] [--keep_tmp] [--ratio]
	                   [--processes NBR] [--reference REFERENCE] [--indent INDENT]
	                   [--sort_keys] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_bundles [in_bundles ...] out_json
	
	Evaluate pairwise similarity measures of bundles.
	All tractograms must be in the same space (aligned to one reference).
	
	Our bundle tractometry analysis scripts
	---------------------------------------
	- scil_bundle_pairwise_comparison:
	    - can compare any pair (any combo) from the input list.
	    - can compare the input list against a single file (--single_compare)
	- scil_bundle_score_many_bundles_one_tractogram:
	    - scores files against their individual ground truth.
	- scil_bundle_score_same_bundle_many_segmentations:
	    - compare many versions of a single bundle.
	* If you have volumes associated to your bundles, the following script could be
	of interest for you: scil_volume_pairwise_comparison
	
	Computed metrics
	----------------
	In this script, metrics can be based on the coverage masks of the bundles or
	directly on the streamlines:
	- For the voxel representation, the computed similarity measures are:
	    bundle_adjacency_voxels, dice_voxels, w_dice_voxels, density_correlation
	    volume_overlap, volume_overreach
	The same measures are also evaluated for the endpoints.
	
	- For the streamline representation, the computed similarity measures are:
	    bundle_adjacency_streamlines, dice_streamlines, streamlines_count_overlap,
	    streamlines_count_overreach
	
	positional arguments:
	  in_bundles            Path of the input bundles.
	  out_json              Path of the output json file.
	
	options:
	  -h, --help            show this help message and exit
	  --streamline_dice     Compute streamline-wise dice coefficient.
	                        Tractograms must be identical [False].
	  --ignore_zeros_in_BA  If set, do not count zeros in the average bundle adjacency (BA).
	  --disable_streamline_distance
	                        Will not compute the streamlines distance 
	                        [False].
	  --single_compare SINGLE_COMPARE
	                        Compare inputs to this single file.
	  --keep_tmp            Will not delete the tmp folder at the end.
	  --ratio               Compute overlap and overreach as a ratio over the reference volume rather than volume.
	                        Can only be used if also using --single_compare`.
	  --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