This is the command cmtk-asegment_sri24 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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