.. _scil_fodf_threshold_by_amplitude:

scil_fodf_threshold_by_amplitude
================================

::

	usage: __main__.py [-h] [--relative RELATIVE] [--absolute ABSOLUTE]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}]
	                   [-f] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_odf out_mask
	
	Compute a binary mask based on a global SF threshold.
	The script masks voxels where the maximum SF amplitude is below
	either a relative factor or an absolute threshold (or both).
	
	When fODFs are evaluated on a sphere (SF), the amplitude of the lobes
	corresponds to the strength of the diffusion signal in those directions.
	Thresholding these amplitudes is a common practice to filter out spurious
	peaks arising from noise or the deconvolution process (e.g., ringing effects).
	
	The absolute threshold can be estimated from the mean/median maximum fODF
	in the ventricles, computed with scil_fodf_max_in_ventricles.
	
	If both --relative and --absolute are provided, the final threshold is the
	maximum of the two resulting values.
	
	positional arguments:
	  in_odf                Input ODF file (SH or Peaks) (.nii.gz).
	  out_mask              Output binary mask (.nii.gz).
	
	options:
	  -h, --help            show this help message and exit
	  --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.
	  --sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}
	                        Dipy sphere; set of possible directions.
	                        Default: [repulsion724]
	  -f                    Force overwriting of the output files.
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	
	Threshold options:
	  --relative RELATIVE   Global SF threshold relative factor (0-1).
	  --absolute ABSOLUTE   Global SF absolute threshold.
	
	2.3.0