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

# cmtk-similarity(1)

Image similarity

## NAME

similarity - Image similarity

## SYNOPSIS

**similarity** Image0 Image1

## DESCRIPTION

Compute similarity measures such as intensity difference or label overlaps between two images.

## 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.

- **--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

- **--outside-bg**

  Assume voxels outside floating image to be background

- **--pad0** *\<double\>*

  Define padding value for reference image **\[Default: disabled\]**

- **--pad1** *\<double\>*

  Define padding value for floating image **\[Default: disabled\]**

- **--grey**, **-g**

  Image pixels are intensities **\[This is the default\]**

- **--labels**, **-l**

  Image pixels are labels

- **--mask** *\<string\>*, **-m** *\<string\>*

  Mask file for optional region-based analysis **\[Default: NONE\]**

- **--force-max** *\<integer\>*

  Force maximum label value **\[Default: 0\]**

- **--histogram-text-file** *\<string\>*

  Output file name for histogram (plain text format). **\[Default: NONE\]**

## 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.