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.