lobe_segment
segment brain lobes using atlas-based label propagation
lobe_segment [options] <classified.mnc> <output_lobes.mnc>
DESCRIPTION
lobe_segment is a Perl script that segments brain lobes from a classified brain volume using template-based lobe definitions. It takes a tissue-classified MINC volume (typically produced by classify) and assigns each voxel to one of the major brain lobes: frontal, parietal, temporal, occipital, and cerebellum.
The segmentation is performed by propagating pre-defined lobe labels from a template atlas to the input volume. The template lobe definitions are stored in a model directory and are mapped onto the subject’s anatomy using the tissue classification as a guide.
The output is a label volume where each voxel is assigned an integer value corresponding to its lobe membership.
OPTIONS
-verbose- Print progress information during processing.
-clobber- Overwrite the output file if it already exists.
-model_dir <dir>- Specify the directory containing template lobe definition files. Defaults to the standard minc-toolkit model directory.
EXAMPLES
Segment brain lobes from a classified volume:
lobe_segment classified.mnc lobes.mnc
Segment with a custom model directory and verbose output:
lobe_segment -verbose -clobber -model_dir /opt/models/lobes classified.mnc lobes.mnc
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © 2009 by Vladimir S. Fonov