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asegment_sri24 - Segmentation using SRI24 atlas

asegment_sri24(1) The Computational Morphometry Toolkit asegment_sri24(1)

NAME

asegment_sri24 - Segmentation using SRI24 atlas

SYNOPSIS

asegment_sri24 TargetImage OutputImage

DESCRIPTION

Register a target image to a selected channel of the SRI24 human brain atlas, then reformat one of the atlas label maps to the target image. Note: it is assume that the target image is skull-stripped, i.e., contains only the brain.

OPTIONS

Global Toolkit Options (these are shared by all CMTK tools)

--help
Write list of basic command line options to standard output.
--help-all
Write complete list of basic and advanced command line options to standard output.
--wiki
Write list of command line options to standard output in MediaWiki markup.
--man
Write man page source in 'nroff' markup to standard output.
--xml
Write command line syntax specification in XML markup (for Slicer integration).
--version
Write toolkit version to standard output.
--echo
Write the current command line to standard output.
--verbose-level <integer>
Set verbosity level.
--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

--fast, -f
Fast mode.
--registration-channel
The SRI24 channel used for registration to the target image. Supported values: "spgr", "early-fse", "late-fse", "fa", where the default is "spgr", or use one of the following:
--spgr
SPGR (T1-weighted) structural channel [This is the default]
--early-fse
Early-echo (PD-weighted) fast spin echo channel
--late-fse
Late-echo (T2-weighted) fast spin echo channel
--fa
Fractional anisotropy channel, derived from diffusion tensor images
--label-map
The SRI24 label map that is reformatted to the target image. Supported values: "tzo116plus", "lpba40", "tissue", where the default is "tzo116plus", or use one of the following:
--tzo116plus
Extended cortical parcellation template based on Tzourio-Mazoyer AAL 116 region template. [This is the default]
--lpba40
Template based on the 40 subject LONI Probabilistic Brain Atlas segmentation.
--tissue
SRI24 maximum likelihood three compartment (GM, WM, CSF) tissue segmentation map.

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

BUGS

Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.
Sep 11 2017 CMTK 3.3.1