---
name: "cmtk-asegment_sri24"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-asegment_sri24"
---

# cmtk-asegment\_sri24(1)

Segmentation using SRI24 atlas

## 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.