lgmask
create a large-structure brain mask for intensity normalization
lgmask [options] <input.mnc> <output_mask.mnc>
DESCRIPTION
lgmask is a Perl script that creates a large-region brain mask from an MRI volume. The mask captures the major brain structures and is intended for use as an initialization step in intensity normalization pipelines.
Unlike a precise brain extraction, lgmask produces a coarse mask that broadly covers the brain region. This is sufficient for estimating intensity normalization parameters where an approximate region of interest is needed rather than an exact brain boundary.
The script uses a combination of thresholding and morphological operations to identify the large brain region from the input volume.
OPTIONS
-verbose- Print progress information during processing.
-clobber- Overwrite the output file if it already exists.
EXAMPLES
Create a large brain mask:
lgmask t1.mnc brain_mask.mnc
Create a mask with verbose output, overwriting existing files:
lgmask -verbose -clobber t1.mnc brain_mask.mnc
AUTHOR
Andrew Janke - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © 2000 by Andrew Janke