.. _scil_fodf_to_bingham:

scil_fodf_to_bingham
====================

::

	usage: __main__.py [-h] [--max_lobes MAX_LOBES] [--at AT] [--rt RT]
	                   [--min_sep_angle MIN_SEP_ANGLE]
	                   [--max_fit_angle MAX_FIT_ANGLE] [--mask MASK]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [--processes NBR] [-f]
	                   in_sh out_bingham
	
	Script for fitting a Bingham distribution to each fODF lobe, as described
	in [1].
	
	The Bingham fit is saved, with each Bingham distribution described by 7
	coefficients (for example, for a maximum number of lobes of 5, the number
	of coefficients is 7 x 5 = 35 -- less than the number of coefficients for
	SH of maximum order 8).
	
	Using 12 threads, the execution takes approximately 30 minutes for a brain with
	1mm isotropic resolution.
	
	-------------------------------------------------------------------------------
	References:
	[1] T. W. Riffert, J. Schreiber, A. Anwander, and T. R. Knösche, “Beyond
	    fractional anisotropy: Extraction of bundle-specific structural metrics
	    from crossing fiber models,” NeuroImage, vol. 100, pp. 176-191, Oct. 2014,
	    doi: 10.1016/j.neuroimage.2014.06.015.
	
	[2] J. Schreiber, T. Riffert, A. Anwander, and T. R. Knösche, “Plausibility
	    Tracking: A method to evaluate anatomical connectivity and microstructural
	    properties along fiber pathways,” NeuroImage, vol. 90, pp. 163-178, Apr.
	    2014, doi: 10.1016/j.neuroimage.2014.01.002.
	-------------------------------------------------------------------------------
	
	positional arguments:
	  in_sh                 Input SH image.
	  out_bingham           Output Bingham functions image.
	
	options:
	  -h, --help            show this help message and exit
	  --max_lobes MAX_LOBES
	                        Maximum number of lobes per voxel to extract. [5]
	  --at AT               Absolute threshold for peaks extraction. [0.0]
	  --rt RT               Relative threshold for peaks extraction. [0.1]
	  --min_sep_angle MIN_SEP_ANGLE
	                        Minimum separation angle between two peaks. [25.0]
	  --max_fit_angle MAX_FIT_ANGLE
	                        Maximum distance in degrees around a peak direction for fitting the Bingham function. [15.0]
	  --mask MASK           Optional mask file. Only SH inside the mask are fitted.
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  --processes NBR       Number of sub-processes to start. 
	                        Default: [1]
	  -f                    Force overwriting of the output files.
	
	2.2.2