.. _scil_bundle_mean_fixel_mrds_metric:

scil_bundle_mean_fixel_mrds_metric
==================================

::

	usage: __main__.py [-h] [--fa FA] [--md MD] [--rd RD] [--ad AD]
	                   [--prefix PREFIX] [--length_weighting]
	                   [--max_theta MAX_THETA] [--reference REFERENCE] [-f]
	                   in_bundle in_pdds
	
	Given a bundle and MRDS metrics, compute the fixel-specific
	metrics at each voxel intersected by the bundle. Intersected voxels are
	found by computing the intersection between the voxel grid and each streamline
	in the input tractogram.
	
	This script behaves like scil_bundle_mean_fixel_afd for fODFs,
	but here for MRDS metrics. These latest distributions add the unique
	possibility to capture fixel-based fractional anisotropy (fixel-FA), mean
	diffusivity (fixel-MD), radial diffusivity (fixel-RD) and
	axial diffusivity (fixel-AD).
	
	Fixel-specific metrics are metrics extracted from
	Multi-Resolution Discrete-Search (MRDS) solutions.
	There are as many values per voxel as there are fixels extracted. The
	values chosen for a given voxel is the one belonging to the lobe better aligned
	with the current streamline segment.
	
	Input files come from scil_mrds_metrics command.
	
	Output metrics will be named: [prefix]_mrds_[metric_name].nii.gz
	
	Please use a bundle file rather than a whole tractogram.
	
	positional arguments:
	  in_bundle             Path of the bundle file.
	  in_pdds               Path of the MRDS PDDs volume.
	
	options:
	  -h, --help            show this help message and exit
	  --prefix PREFIX       Prefix of the MRDS fixel results.
	  --length_weighting    If set, will weight the values according to segment lengths. [False]
	  --max_theta MAX_THETA
	                        Maximum angle (in degrees) condition on fixel alignment. [60]
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	  -f                    Force overwriting of the output files.
	
	MRDS metrics input:
	  --fa FA               Path of the fixel-specific metric FA volume.
	  --md MD               Path of the fixel-specific metric MD volume.
	  --rd RD               Path of the fixel-specific metric RD volume.
	  --ad AD               Path of the fixel-specific metric AD volume.
	
	2.2.2