cmtk-asegment_sri241

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.