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¶
- --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).
