.. _scil_NODDI_priors:

scil_NODDI_priors
=================

::

	usage: __main__.py [-h] [--fa_min_single_fiber FA_MIN_SINGLE_FIBER]
	                   [--fa_max_ventricles FA_MAX_VENTRICLES]
	                   [--md_min_ventricles MD_MIN_VENTRICLES]
	                   [--roi_radius ROI_RADIUS] [--roi_center pos pos pos]
	                   [--out_txt_1fiber_para FILE] [--out_txt_1fiber_perp FILE]
	                   [--out_mask_1fiber FILE] [--out_txt_ventricles FILE]
	                   [--out_mask_ventricles FILE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_FA in_AD in_RD in_MD
	
	Compute the axial (para_diff), radial (perp_diff), and mean (iso_diff)
	diffusivity priors for NODDI.
	
	---------------------------------------------------------------
	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_FA                 Path to the FA volume.
	  in_AD                 Path to the axial diffusivity (AD) volume.
	  in_RD                 Path to the radial diffusivity (RD) volume.
	  in_MD                 Path to the mean diffusivity (MD) volume.
	
	options:
	  -h, --help            show this help message and exit
	  -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.
	
	Metrics options:
	  --fa_min_single_fiber FA_MIN_SINGLE_FIBER
	                        Minimal threshold of FA (voxels above that threshold are considered in 
	                        the single fiber mask). [0.7]
	  --fa_max_ventricles FA_MAX_VENTRICLES
	                        Maximal threshold of FA (voxels under that threshold are considered in 
	                        the ventricles). [0.1]
	  --md_min_ventricles MD_MIN_VENTRICLES
	                        Minimal threshold of MD in mm2/s (voxels above that threshold are considered 
	                        for in the ventricles). [0.003]
	
	Regions options:
	  --roi_radius ROI_RADIUS
	                        Radius of the region used to estimate the priors. The roi will be a cube spanning 
	                        from ROI_CENTER in each direction. [20]
	  --roi_center pos pos pos
	                        Center of the roi of size roi_radius used to estimate the priors; a 3-value coordinate. 
	                        If not set, uses the center of the 3D volume.
	
	Outputs:
	  --out_txt_1fiber_para FILE
	                        Output path for the text file containing the single fiber average value of AD.
	                        If not set, the file will not be saved.
	  --out_txt_1fiber_perp FILE
	                        Output path for the text file containing the single fiber average value of RD.
	                        If not set, the file will not be saved.
	  --out_mask_1fiber FILE
	                        Output path for single fiber mask. If not set, the mask will not be saved.
	  --out_txt_ventricles FILE
	                        Output path for the text file containing the ventricles average value of MD.
	                        If not set, the file will not be saved.
	  --out_mask_ventricles FILE
	                        Output path for the ventricule mask.
	                        If not set, the mask will not be saved.
	
	2.2.2