.. _scil_fodf_max_in_ventricles:

scil_fodf_max_in_ventricles
===========================

::

	usage: __main__.py [-h] [--fa_threshold FA_THRESHOLD]
	                   [--md_threshold MD_THRESHOLD] [--in_mask file]
	                   [--max_value_output file] [--out_mask file] [--small_dims]
	                   [--use_median]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   fODFs FA MD
	
	Script to compute the mean/median maximum fODF in the ventricles. The
	ventricules are estimated from an MD and FA threshold.
	
	This allows to clip the noise of fODF using an absolute thresold.
	
	--------------------------------------------------------------------------
	Reference:
	[1] Dell'Acqua, Flavio, et al. "Can spherical deconvolution provide more
	    information than fiber orientations? Hindrance modulated orientational
	    anisotropy, a true-tract specific index to characterize white matter
	    diffusion." Human brain mapping 34.10 (2013): 2464-2483.
	--------------------------------------------------------------------------
	
	positional arguments:
	  fODFs                 Path of the fODF volume in spherical harmonics (SH).
	  FA                    Path to the FA volume.
	  MD                    Path to the mean diffusivity (MD) volume.
	
	options:
	  -h, --help            show this help message and exit
	  --fa_threshold FA_THRESHOLD
	                        Maximal threshold of FA (voxels under that threshold are considered 
	                        for evaluation. [0.1]).
	  --md_threshold MD_THRESHOLD
	                        Minimal threshold of MD in mm2/s (voxels above that threshold are 
	                        considered for evaluation. [0.003]).
	  --in_mask file        Path to a binary mask. Only the data inside the mask will be used 
	                        for evaluation. Useful if the FA and MD thresholds are not good enough.
	  --max_value_output file
	                        Output path for the text file containing the value. If not set the 
	                        file will not be saved.
	  --out_mask file       Output path for the ventricule mask. If not set, the mask 
	                        will not be saved.
	  --small_dims          If set, takes the full range of data to search the max fodf amplitude 
	                        in ventricles. Useful when the data has small dimensions.
	  --use_median          If set, use the median value instead of the mean.
	  --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.
	  -f                    Force overwriting of the output files.
	
	2.2.2