usage: __main__.py [-h] [--include filename] [--exclude filename]
[--interface filename] [-t THRESHOLD] [-f]
[-v [{DEBUG,INFO,WARNING}]]
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.
Formerly: scil_compute_maps_for_particle_filter_tracking.py
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}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.