.. _scil_mrds_metrics:

scil_mrds_metrics
=================

::

	usage: __main__.py [-h] [--mask MASK] [--not_all] [--fa file] [--ad file]
	                   [--rd file] [--md file] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_evals
	
	Script to compute FA/MD/RD/AD for
	each Multi-ResolutionDiscrete-Search (MRDS) solution.
	It will output the results in 4 different 4D files.
	Each 4th dimension will correspond to each tensor in the MRDS solution.
	e.g. FA of tensor D_1 will be in index 0 of the 4th dimension,
	     FA of tensor D_2 will be in index 1 of the 4th dimension,
	     FA of tensor D_3 will be in index 2 of the 4th dimension.
	
	positional arguments:
	  in_evals              MRDS eigenvalues file (Shape: [X, Y, Z, 9]).
	                        The last dimensions, values 1-3 are associated with the first tensor (D_1), 4-6 with the second tensor (D_2), 7-9 with the third tensor (D_3).
	                        This file is one of the outputs of scil_mrds_select_number_of_tensors (*_MRDS_evals.nii.gz).
	
	options:
	  -h, --help            show this help message and exit
	  --mask MASK           Path to a binary mask.
	                        Only data inside the mask will be used for computations and reconstruction. (Default: None)
	  --not_all             If set, will only save the metrics explicitly specified using the other metrics flags. (Default: not set).
	  -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.
	
	MRDS-Metrics files flags:
	  --fa file             Output filename for the FA.
	  --ad file             Output filename for the AD.
	  --rd file             Output filename for the RD.
	  --md file             Output filename for the MD.
	
	2.2.2