xenial (1) cmtk-asegment_sri24.1.gz

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.