pipeline_thomas.pl
tissue-class Jacobian-modulated blurred maps for THOMAS
pipeline_thomas.pl <cls> <nl_xfm> <jacobian> <out_csf> <out_gm> <out_wm>
DESCRIPTION
pipeline_thomas.pl generates tissue-class-specific Jacobian-modulated and blurred maps suitable for use with the THOMAS (Thalamus Optimized Multi-Atlas Segmentation) pipeline or similar voxel-based analyses. For each tissue class (CSF, GM, WM), the script extracts a binary mask from the classification, modulates it by the Jacobian determinant of the nonlinear transformation, and applies spatial smoothing.
The resulting maps encode both tissue presence and local volume information, making them suitable for statistical analyses of regional brain volume differences.
OPTIONS
--verbose- Print progress information during processing.
--clobber- Overwrite output files if they already exist.
EXAMPLES
Generate THOMAS tissue maps:
pipeline_thomas.pl classified.mnc nl.xfm jacobian.mnc \
csf_thomas.mnc gm_thomas.mnc wm_thomas.mnc
Generate with verbose output and clobber:
pipeline_thomas.pl classified.mnc nl.xfm jacobian.mnc \
csf_thomas.mnc gm_thomas.mnc wm_thomas.mnc --verbose --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.