.. _scil_bundle_mean_fixel_afd_from_hdf5:

scil_bundle_mean_fixel_afd_from_hdf5
====================================

::

	usage: __main__.py [-h] [--length_weighting] [--processes NBR]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_hdf5 in_fodf out_hdf5
	
	Compute the mean Apparent Fiber Density (AFD) and mean Radial fODF (radfODF)
	maps for every connections within a hdf5 (.h5) file.
	
	This is the "real" fixel-based fODF amplitude along every streamline
	of each connection, averaged at every voxel.
	
	Please use a hdf5 (.h5) file containing decomposed connections
	
	----------------------------------------------------------------------------
	Reference:
	[1] Raffelt, D., Tournier, JD., Rose, S., Ridgway, GR., Henderson, R.,Crozier,
	    S., Salvado, O., & Connelly, A. (2012). Apparent Fibre Density: a novel
	    measure for the analysis of diffusion-weighted magnetic resonance images.
	    NeuroImage, 59(4), 3976--3994.
	----------------------------------------------------------------------------
	
	positional arguments:
	  in_hdf5               HDF5 filename (.h5) containing decomposed connections.
	  in_fodf               Path of the fODF volume in spherical harmonics (SH).
	  out_hdf5              Path of the output HDF5 filenames (.h5).
	
	options:
	  -h, --help            show this help message and exit
	  --length_weighting    If set, will weigh the AFD values according to segment lengths. [False]
	  --processes NBR       Number of sub-processes to start. 
	                        Default: [1]
	  --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