.. _scil_connectivity_pairwise_agreement:

scil_connectivity_pairwise_agreement
====================================

::

	usage: __main__.py [-h] [--single_compare matrix] [--normalize]
	                   [--indent INDENT] [--sort_keys]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_matrices [in_matrices ...] out_json
	
	Evaluate pair-wise similarity measures of connectivity matrices.
	
	The computed similarity measures are:
	- RMSE: root-mean-square difference
	- Pearson correlation coefficent
	- w-dice: weighted dice, agreement of the values.
	- dice: agreement of the binarized matrices
	
	If more than two matrices are given in input, the similarity measures will be
	computed for each pair. Alternatively, you can compare all matrices to a
	single reference, using --single_compare.
	
	positional arguments:
	  in_matrices           Path of the input matricies.
	  out_json              Path of the output json file.
	
	options:
	  -h, --help            show this help message and exit
	  --single_compare matrix
	                        Compare inputs to this single file.
	                        (Else, compute all pairs in in_matrices).
	  --normalize           If set, will normalize all matrices from zero to one.
	  -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