.. _scil_bundle_generate_priors:

scil_bundle_generate_priors
===========================

::

	usage: __main__.py [-h]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [--todi_sigma {0,1,2,3,4}] [--sf_threshold SF_THRESHOLD]
	                   [--out_prefix OUT_PREFIX] [--out_dir OUT_DIR]
	                   [--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_bundle in_fodf in_mask
	
	Generation of priors and enhanced-FOD from an example/template bundle.
	The bundle must have been cleaned thorougly before use. The E-FOD can then
	be used for bundle-specific tractography, but not for FOD metrics.
	
	-----------------------------------------------------------------------------
	Reference:
	[1] Rheault, Francois, et al. "Bundle-specific tractography with incorporated
	    anatomical and orientational priors." NeuroImage 186 (2019): 382-398
	-----------------------------------------------------------------------------
	
	positional arguments:
	  in_bundle             Input bundle filename.
	  in_fodf               Input FOD filename.
	  in_mask               Mask to constrain the TODI spatial smoothing,
	                        for example a WM mask.
	
	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.
	  --todi_sigma {0,1,2,3,4}
	                        Smooth the orientation histogram.
	  --sf_threshold SF_THRESHOLD
	                        Relative threshold for sf masking (0.0-1.0).
	  --out_prefix OUT_PREFIX
	                        Add a prefix to all output filenames, default is no prefix.
	                        The generated files are: 
	                        - efod: the enhanced FOD
	                        - priors
	                        - todi_mask
	                        - endpoints_mask: a binary mask.
	  --out_dir OUT_DIR     Output directory for all generated files,
	                        default is current directory.
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	  -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