pipeline_segment.pl

lobe segmentation using atlas templates

pipeline_segment.pl <classified> <lin_xfm> <nl_xfm> <output_lobes> [options]

DESCRIPTION

pipeline_segment.pl performs brain lobe segmentation by propagating atlas labels through linear and nonlinear transformations to the subject space. The script takes a tissue classification volume and both linear and nonlinear transforms mapping the subject to the atlas, then produces a lobe segmentation volume where each voxel is labelled with its anatomical lobe (frontal, temporal, parietal, occipital, etc.).

The segmentation is constrained by the tissue classification so that only brain voxels receive lobe labels. A custom template can be specified with the –template option to use alternative atlas definitions.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite the output file if it already exists.

--model-dir <dir>

Path to the directory containing the atlas model and template files.

--template <file>

Atlas lobe template file to use for segmentation. If not specified, the default template from the model directory is used.

EXAMPLES

Segment brain lobes with default template:

pipeline_segment.pl classified.mnc tal.xfm nl.xfm lobes.mnc \
  --model-dir /opt/minc/share/icbm152_model_09c

Segment with a custom template:

pipeline_segment.pl classified.mnc tal.xfm nl.xfm lobes.mnc \
  --model-dir /opt/minc/share/icbm152_model_09c \
  --template custom_lobes.mnc

Segment with verbose output and clobber:

pipeline_segment.pl classified.mnc tal.xfm nl.xfm lobes.mnc \
  --model-dir /opt/minc/share/icbm152_model_09c --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.

SEE ALSO

lobe_segment.pl