.. _scil_tracking_pft_maps:

scil_tracking_pft_maps
======================

::

	usage: __main__.py [-h] [--include filename] [--exclude filename]
	                   [--interface filename] [-t THRESHOLD] [-f]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_wm in_gm in_csf
	
	Compute include and exclude maps, and the seeding interface mask from partial
	volume estimation (PVE) maps. Maps should have values in [0,1], gm+wm+csf=1 in
	all voxels of the brain, gm+wm+csf=0 elsewhere.
	
	References: Girard, G., Whittingstall K., Deriche, R., and Descoteaux, M.
	(2014). Towards quantitative connectivity analysis: reducing tractography
	biases. Neuroimage.
	
	-----------------------------------------------------------------------------
	Reference:
	[1] Girard, G., Whittingstall K., Deriche, R., and Descoteaux, M. (2014).
	    Towards quantitative connectivity analysis: reducing tractographybiases.
	    Neuroimage.
	-----------------------------------------------------------------------------
	
	positional arguments:
	  in_wm                 White matter PVE map (nifti). From normal FAST output, has a PVE_2 name suffix.
	  in_gm                 Grey matter PVE map (nifti). From normal FAST output, has a PVE_1 name suffix.
	  in_csf                Cerebrospinal fluid PVE map (nifti). From normal FAST output, has a PVE_0 name suffix.
	
	options:
	  -h, --help            show this help message and exit
	  --include filename    Output include map (nifti). [map_include.nii.gz]
	  --exclude filename    Output exclude map (nifti). [map_exclude.nii.gz]
	  --interface filename  Output interface seeding mask (nifti). [interface.nii.gz]
	  -t THRESHOLD          Minimum gm and wm PVE values in a voxel to be into the interface. [0.1]
	  -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.
	
	2.2.2