lobe_segment.pl

segment brain lobes using atlas-based label propagation

lobe_segment [options] <to_model_nl.xfm> <to_tal.xfm> <class.mnc> <out_labels.mnc>

DESCRIPTION

lobe_segment performs stereotaxic lobe segmentation of a classified brain volume using atlas-based label propagation. It takes as input the nonlinear transformation to model space, the linear transformation to Talairach space, and a tissue classification volume (e.g. from classify), and produces a labelled output volume where each voxel is assigned to a brain lobe.

The tool uses atlas templates in the model directory to propagate lobe labels from the atlas to the subject. A cortical surface mask can optionally be provided for refined segmentation at grey/white boundaries.

OPTIONS

-version: Print version information and exit.
-surface_mask <obj>: Use the specified cortical surface object as a mask for surface-based refinement of lobe boundaries.
-template <mnc>: Use the specified MINC volume as the atlas template instead of the default.
-modeldir <dir>: Path to the directory containing atlas label templates.
-gwcb <g w c b>: Set the label values for grey matter, white matter, CSF, and background in the tissue classification input. Default: 2 3 1 0.
-verbose: Print progress information during processing.
-debug: Print additional debugging information.
-clobber: Overwrite existing output files.
-tmpdir <dir>: Use the specified directory for temporary files.
-keeptmp: Do not delete temporary files after completion.

EXAMPLES

Segment lobes from a classified brain volume:

lobe_segment subject_to_model_nl.xfm subject_to_tal.xfm \
    classify.mnc lobes.mnc

Segment lobes with a custom model directory and surface mask:

lobe_segment -modeldir /opt/models/lobe_atlas \
    -surface_mask cortex.obj \
    subject_to_model_nl.xfm subject_to_tal.xfm \
    classify.mnc lobes.mnc

Segment with non-default tissue class labels:

lobe_segment -gwcb 1 2 3 0 -verbose -clobber \
    subject_to_model_nl.xfm subject_to_tal.xfm \
    classify.mnc lobes.mnc

AUTHOR

Jason Lerch, Vladimir S. Fonov. McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

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