debian man page for cmtk-asegment_sri24

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, and Daniel B. Russakoff

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

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

ACKNOWLEDGMENTS
       From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging  and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 						 asegment_sri24(1)