.. _scil_bingham_metrics:

scil_bingham_metrics
====================

::

	usage: __main__.py [-h] [--out_fd OUT_FD] [--out_fs OUT_FS] [--out_ff OUT_FF]
	                   [--not_all] [--mask MASK]
	                   [--nbr_integration_steps NBR_INTEGRATION_STEPS]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [--processes NBR] [-f]
	                   in_bingham
	
	Script to compute fODF lobe-specific metrics derived from a Bingham
	distribution fit, as described in [1]. Resulting metrics are fiber density
	(FD), fiber spread (FS) and fiber fraction (FF) [2].
	
	The Bingham coefficients volume comes from scil_fodf_to_bingham.
	
	A lobe's FD is the integral of the Bingham function on the sphere. It
	represents the density of fibers going through a given voxel for a given
	fODF lobe (fixel). A lobe's FS is the ratio of its FD on its maximum AFD. It
	is at its minimum for a sharp lobe and at its maximum for a wide lobe. A lobe's
	FF is the ratio of its FD on the total FD in the voxel.
	
	Using 12 threads, the execution takes 10 minutes for FD estimation for a brain
	with 1mm isotropic resolution. Other metrics take less than a second.
	
	------------------------------------------------------------------------------
	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_bingham            Input Bingham nifti image.
	
	options:
	  -h, --help            show this help message and exit
	  --out_fd OUT_FD       Path to output fiber density. [fd.nii.gz]
	  --out_fs OUT_FS       Path to output fiber spread. [fs.nii.gz]
	  --out_ff OUT_FF       Path to fiber fraction file. [ff.nii.gz]
	  --not_all             Do not compute all metrics. Then, please provide the output paths of the files you need.
	  --mask MASK           Optional mask image. Only voxels inside the mask are computed.
	  --nbr_integration_steps NBR_INTEGRATION_STEPS
	                        Number of integration steps along the theta axis for fiber density estimation. [50]
	  -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