pipeline_volumes_nl.pl
compute brain and lobe volumes from nonlinear registration
pipeline_volumes_nl.pl <mask> <cls> <lobes> <xfm> <output.txt> [options]
DESCRIPTION
pipeline_volumes_nl.pl computes brain tissue volumes on a per-lobe basis using nonlinear registration results. In addition to the global tissue volumes computed by pipeline_volumes_lin.pl, this script uses the lobe segmentation to break down volumes by anatomical region (frontal, temporal, parietal, occipital lobes, etc.).
The script takes a brain mask, tissue classification, lobe segmentation volume, and the nonlinear transform, and produces a text file with detailed volumetric measurements. Volumes are corrected using the Jacobian determinant of the nonlinear transform to report values in native-space cubic millimetres.
OPTIONS
--verbose- Print progress information during processing.
--clobber- Overwrite the output file if it already exists.
--age <n>- Subject age in years, included as metadata in the output file.
--gender <M|F>- Subject gender, included as metadata in the output file.
--scanner <name>- Scanner model or identifier, included as metadata in the output file.
--scanner_id <id>- Scanner serial number or unique identifier, included as metadata in the output file.
--t1 <file>- Path to the T1-weighted input volume, recorded in the output file.
--t2 <file>- Path to the T2-weighted input volume, recorded in the output file.
--pd <file>- Path to the proton-density input volume, recorded in the output file.
EXAMPLES
Compute lobe-based tissue volumes:
pipeline_volumes_nl.pl brain_mask.mnc classified.mnc lobes.mnc \
nl.xfm volumes_nl.txt
Compute volumes with demographic metadata:
pipeline_volumes_nl.pl brain_mask.mnc classified.mnc lobes.mnc \
nl.xfm volumes_nl.txt --age 65 --gender F \
--scanner GE_Discovery --scanner_id G001
Compute volumes with input file references and clobber:
pipeline_volumes_nl.pl brain_mask.mnc classified.mnc lobes.mnc \
nl.xfm volumes_nl.txt \
--t1 t1_native.mnc --t2 t2_native.mnc --pd pd_native.mnc --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.