.. _scil_freewater_maps:

scil_freewater_maps
===================

::

	usage: __main__.py [-h] [--mask MASK] [--out_dir OUT_DIR] [--b_thr B_THR]
	                   [--para_diff PARA_DIFF] [--iso_diff ISO_DIFF]
	                   [--perp_diff_min PERP_DIFF_MIN]
	                   [--perp_diff_max PERP_DIFF_MAX] [--lambda1 LAMBDA1]
	                   [--lambda2 LAMBDA2]
	                   [--save_kernels DIRECTORY | --load_kernels DIRECTORY]
	                   [--compute_only] [--mouse] [--processes NBR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec
	
	Compute Free Water maps [1] using the AMICO framework [2].
	This script supports both single and multi-shell data.
	
	----------------------------------------------------------
	References:
	[1] Pasternak 0, Sochen N, Gur Y, Intrator N, Assaf Y.
	    Free water elimination and mapping from diffusion mri.
	    Magn Reson Med. 62 (3) (2009) 717-730.
	[2] Daducci A, et al. Accelerated microstructure imaging
	    via convex optimization (AMICO) from diffusion MRI data.
	    Neuroimage 105 (2015) 32-44.
	----------------------------------------------------------
	
	positional arguments:
	  in_dwi                DWI file.
	  in_bval               b-values filename, in FSL format (.bval).
	  in_bvec               b-vectors filename, in FSL format (.bvec).
	
	options:
	  -h, --help            show this help message and exit
	  --mask MASK           Brain mask filename.
	  --out_dir OUT_DIR     Output directory for the Free Water results. [results]
	  --b_thr B_THR         Limit value to consider that a b-value is on an existing shell. Above this limit, the b-value is placed on a new shell. This includes b0s values.
	  --mouse               If set, use mouse fitting profile.
	  --processes NBR       Number of sub-processes to start. 
	                        Default: [1]
	  -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.
	
	Model options:
	  --para_diff PARA_DIFF
	                        Axial diffusivity (AD) in the CC. [0.0015]
	  --iso_diff ISO_DIFF   Mean diffusivity (MD) in ventricles. [0.003]
	  --perp_diff_min PERP_DIFF_MIN
	                        Radial diffusivity (RD) minimum. [0.0001]
	  --perp_diff_max PERP_DIFF_MAX
	                        Radial diffusivity (RD) maximum. [0.0007]
	  --lambda1 LAMBDA1     First regularization parameter. [0.0]
	  --lambda2 LAMBDA2     Second regularization parameter. [0.25]
	
	Kernels options:
	  --save_kernels DIRECTORY
	                        Output directory for the COMMIT kernels.
	  --load_kernels DIRECTORY
	                        Input directory where the COMMIT kernels are located.
	  --compute_only        Compute kernels only, --save_kernels must be used.
	
	2.2.2