asegment_sri24 - Segmentation using SRI24 atlas
asegment_sri24 TargetImage OutputImage
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.
- --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).
- --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.
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg
Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
http://www.fsf.org/licensing/licenses/gpl.html
Report bugs at http://nitrc.org/projects/cmtk/
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.