.. _scil_fodf_metrics:

scil_fodf_metrics
=================

::

	usage: __main__.py [-h] [--sphere string] [--mask] [--at A_THRESHOLD]
	                   [--rt R_THRESHOLD] [--abs_peaks_and_values]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [--processes NBR] [-f]
	                   [--not_all] [--afd_max file] [--afd_total file]
	                   [--afd_sum file] [--nufo file] [--rgb file] [--peaks file]
	                   [--peak_values file] [--peak_indices file]
	                   in_fODF
	
	Script to compute the maximum Apparent Fiber Density (AFD), the fiber ODFs
	orientations, values and indices (peaks, peak_values, peak_indices), the Number
	of Fiber Orientations (NuFO) maps from fiber ODFs and the RGB map.
	
	AFD_max map is the maximal fODF amplitude for each voxel.
	
	NuFO is the the number of maxima of the fODF with an ABSOLUTE amplitude above
	the threshold set using --at, AND an amplitude above the RELATIVE threshold
	set using --rt.
	
	The --at argument should be set to a value which is 1.5 times the maximal
	value of the fODF in the ventricules. This can be obtained with the
	scil_fodf_max_in_ventricles script.
	
	If the --abs_peaks_and_values argument is set, the peaks are all normalized
	and the peak_values are equal to the actual fODF amplitude of the peaks. By
	default, the script max-normalizes the peak_values for each voxel and
	multiplies the peaks by peak_values.
	
	By default, will output all possible files, using default names. Specific names
	can be specified using the file flags specified in the "File flags" section.
	
	If --not_all is set, only the files specified explicitly by the flags will be
	output.
	
	See [Raffelt et al. NeuroImage 2012] and [Dell'Acqua et al HBM 2013] for the
	definitions.
	
	positional arguments:
	  in_fODF               Path of the fODF volume in spherical harmonics (SH).
	
	options:
	  -h, --help            show this help message and exit
	  --sphere string       Discrete sphere to use in the processing [repulsion724].
	  --mask                Path to a binary mask. Only the data inside the mask
	                        will beused for computations and reconstruction [None].
	  --at A_THRESHOLD      Absolute threshold on fODF amplitude. This value should be set to
	                        approximately 1.5 to 2 times the maximum fODF amplitude in isotropic voxels
	                        (ie. ventricles).
	                        Use scil_fodf_max_in_ventricles to find the maximal value.
	                        See [Dell'Acqua et al HBM 2013] [0.0].
	  --rt R_THRESHOLD      Relative threshold on fODF amplitude in percentage  [0.1].
	  --abs_peaks_and_values
	                        If set, the peak_values are not max-normalized for each voxel, 
	                        but rather they keep the actual fODF amplitude of the peaks. 
	                        Also, the peaks are given as unit directions instead of being proportional to peak_values. [False]
	  --sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}
	                        Spherical harmonics basis used for the SH coefficients. 
	                        Must be either descoteaux07', 'tournier07', 
	                        'descoteaux07_legacy' or 'tournier07_legacy' [['descoteaux07_legacy']]:
	                            'descoteaux07'       : SH basis from the Descoteaux et al.
	                                                   MRM 2007 paper
	                            'tournier07'         : SH basis from the new Tournier et al.
	                                                   NeuroImage 2019 paper, as in MRtrix 3.
	                            'descoteaux07_legacy': SH basis from the legacy Dipy implementation
	                                                   of the Descoteaux et al. MRM 2007 paper
	                            'tournier07_legacy'  : SH basis from the legacy Tournier et al.
	                                                   NeuroImage 2007 paper.
	  -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.
	  --not_all             If set, only saves the files specified using the file flags [False].
	
	File flags:
	  --afd_max file        Output filename for the AFD_max map.
	  --afd_total file      Output filename for the AFD_total map(SH coeff = 0).
	  --afd_sum file        Output filename for the sum of all peak contributions
	                        (sum of fODF lobes on the sphere).
	  --nufo file           Output filename for the NuFO map.
	  --rgb file            Output filename for the RGB map.
	  --peaks file          Output filename for the extracted peaks.
	  --peak_values file    Output filename for the extracted peaks values.
	  --peak_indices file   Output filename for the generated peaks indices on the sphere.
	
	2.2.2