.. _scil_fibertube_score_tractogram:

scil_fibertube_score_tractogram
===============================

::

	usage: __main__.py [-h] [--save_error_tractogram]
	                   [--out_tracked_fibertubes OUT_TRACKED_FIBERTUBES]
	                   [--indent INDENT] [--sort_keys]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_fibertubes in_tracking in_config out_metrics
	
	Given ground-truth fibertubes and a tractogram obtained through fibertube
	tracking, computes metrics about the quality of individual fiber
	reconstruction.
	
	Each streamline is associated with an "Termination fibertube segment", which is
	the closest fibertube segment to its before-last coordinate. We then define
	the following terms:
	
	VC: "Valid Connection": A streamline whose termination fibertube segment is
	the final segment of the fibertube in which is was originally seeded.
	
	IC: "Invalid Connection": A streamline whose termination fibertube segment is
	the start or final segment of a fibertube in which is was not seeded.
	
	NC: "No Connection": A streamline whose termination fibertube segment is
	not the start or final segment of any fibertube.
	
	The "absolute error" of a coordinate is the distance in mm between that
	coordinate and the closest point on its corresponding fibertube. The average
	of all coordinate absolute errors of a streamline is called the "Mean absolute
	error" or "mae".
	
	Computed metrics:
	    - vc_ratio
	        Number of VC divided by the number of streamlines.
	    - ic_ratio
	        Number of IC divided by the number of streamlines.
	    - nc_ratio
	        Number of NC divided by the number of streamlines.
	    - mae_min
	        Minimum MAE for the tractogram.
	    - mae_max
	        Maximum MAE for the tractogram.
	    - mae_mean
	        Average MAE for the tractogram.
	    - mae_med
	        Median MAE for the tractogram.
	
	See also:
	    - scil_tractogram_filter_collisions to prepare data for fibertube
	      tracking
	    - scil_fibertube_tracking to perform a fibertube tracking
	    - docs/source/documentation/fibertube_tracking.rst
	
	positional arguments:
	  in_fibertubes         Path to the tractogram (must be .trk) file 
	                        containing fibertubes. They must have their 
	                        respective diameter saved as data_per_streamline.
	  in_tracking           Path to the tractogram file (must be .trk) 
	                        containing the reconstruction of ground-truth 
	                        fibertubes made from fibertube tracking. Seeds 
	                        used for tracking must be saved as 
	                        data_per_streamline.
	  in_config             Path to a json file containing the fibertube 
	                        parameters used for the tracking process.
	  out_metrics           Output file containing the computed measures and 
	                        metrics (must be .json).
	
	options:
	  -h, --help            show this help message and exit
	  --save_error_tractogram
	                        If set, a .trk file will be saved, containing a 
	                        visual representation of all the coordinate absolute 
	                        errors of the entire tractogram. The file name is 
	                        derived from the out_metrics parameter.
	  --out_tracked_fibertubes OUT_TRACKED_FIBERTUBES
	                        If set, the fibertubes that were used for seeding will be 
	                        saved separately at the specified location (must be .trk or 
	                        .tck). This parameter is not required for scoring the tracking 
	                        result, as the seeding information of each streamline is always 
	                        saved as data_per_streamline.
	  -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