.. _scil_NODDI_maps:

scil_NODDI_maps
===============

::

	usage: __main__.py [-h] [--mask MASK] [--out_dir OUT_DIR] [--tolerance tol]
	                   [--skip_b0_check] [--para_diff PARA_DIFF]
	                   [--iso_diff ISO_DIFF] [--lambda1 LAMBDA1]
	                   [--lambda2 LAMBDA2]
	                   [--save_kernels DIRECTORY | --load_kernels DIRECTORY]
	                   [--compute_only] [--processes NBR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec
	
	Compute NODDI [1] maps using AMICO.
	Multi-shell DWI necessary.
	
	---------------------------------------------------------------
	Reference:
	[1] Zhang H, Schneider T, Wheeler-Kingshott CA, Alexander DC.
	    NODDI: practical in vivo neurite orientation dispersion
	    and density imaging of the human brain.
	    NeuroImage. 2012 Jul 16;61:1000-16.
	---------------------------------------------------------------
	
	positional arguments:
	  in_dwi                DWI file acquired with a NODDI compatible protocol (single-shell data not suited).
	  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 NODDI results. [results]
	  --tolerance tol       The tolerated gap between the b-values to extract and the current b-value.
	                        [Default: 20]
	                        * Note. We would expect to find at least one b-value in the 
	                          range [0, tolerance]. To skip this check, use --skip_b0_check.
	  --skip_b0_check       By default, we supervise that at least one b0 exists in your data
	                        (i.e. b-values below the default --tolerance). Use this option to 
	                        allow continuing even if the minimum b-value is suspiciously high.
	                        If no b-value is found below the threshold, the script will continue 
	                        with the original --tolerance and no b0 volumes.
	                        Use with care, and only if you understand your data.
	  --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]
	  --lambda1 LAMBDA1     First regularization parameter. [0.5]
	  --lambda2 LAMBDA2     Second regularization parameter. [0.001]
	
	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