pipeline_smooth.pl
smooth tissue probability maps with optional Jacobian modulation
pipeline_smooth.pl <cls> <out_wm> <out_gm> <out_csf> [out_lj] [options]
DESCRIPTION
pipeline_smooth.pl generates smoothed tissue probability maps from a discrete tissue classification volume. For each tissue class (white matter, grey matter, cerebrospinal fluid), a binary map is extracted from the classification and blurred with a Gaussian kernel to produce a smooth probability map.
When a nonlinear transform is provided via –xfm, the tissue maps can be modulated by the Jacobian determinant of the transformation. This Jacobian modulation preserves information about local volume differences, producing maps suitable for voxel-based morphometry (VBM) analysis. The optional fourth output receives the log-Jacobian-modulated maps.
OPTIONS
--verbose- Print progress information during processing.
--clobber- Overwrite output files if they already exist.
--fwhm <f>- Full-width at half-maximum of the Gaussian smoothing kernel in millimetres. Default is 8.
--xfm <file>- Nonlinear transformation file whose Jacobian determinant is used to modulate the tissue probability maps.
EXAMPLES
Smooth tissue maps with default 8 mm kernel:
pipeline_smooth.pl classified.mnc wm_smooth.mnc gm_smooth.mnc csf_smooth.mnc
Smooth with 6 mm kernel and Jacobian modulation:
pipeline_smooth.pl classified.mnc wm_smooth.mnc gm_smooth.mnc \
csf_smooth.mnc lj_smooth.mnc --fwhm 6 --xfm nl.xfm
Smooth with clobber:
pipeline_smooth.pl classified.mnc wm_smooth.mnc gm_smooth.mnc \
csf_smooth.mnc --clobber
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.