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

# cmtk-mcaffine(1)

Multi-channel affine registration

## NAME

mcaffine - Multi-channel affine registration

## SYNOPSIS

mcaffine \[options\] refChannel0 \[refChannel1 ...\] -- fltChannel0 \[fltChannel1 ...\]

## DESCRIPTION

Multi-channel affine image registration using histogram-based or covariance-based joint entropy measures

## 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

- **--out-archive** *\<string\>*, **-o** *\<string\>*

  Output archive path. **\[Default: NONE\]**

- **--initial-xform** *\<string\>*

  Optional path of a file with the initial transformation. **\[Default: NONE\]**

- **--downsample-from** *\<integer\>*, **-d** *\<integer\>*

  Initial downsampling factor \[1\]. **\[Default: 1\]**

- **--downsample-to** *\<integer\>*, **-D** *\<integer\>*

  Final downsampling factor \[1\]. Factor 0 is full resolution with smoothing turned off **\[Default: 1\]**

- **--smooth** *\<float\>*

  Sigma of Gaussian smoothing kernel in multiples of template image pixel size \[default: off\] ) **\[Default: 0\]**

- **--downsample-average** *\<boolean\>*

  Downsample using sliding-window averaging \[default: off\] ) **\[Default: 0\]**

- **--dofs** *\<integer\>\[,\<integer\>,...\]*

  Set sequence of numbers of DOFs for optimization schedule \[can be repeated\]. Supported values are: 0, 3, 6, 7, 9, 12.

- **--nmi**

  Use normalized mutual information metric \[default\] **\[This is the default\]**

- **--mi**

  Use standard mutual information metric

- **--histograms**, **-H**

  Use multi-dimensional histograms to compute entropies \[default\] **\[This is the default\]**

- **--covariance**, **-C**

  Use covariance matrix determinants to compute entropies

- **--cubic**, **-c**

  Use cubic interpolation \[default: linear\]

- **--initial-step-size** *\<double\>*

  Initial optimizer step size in pixels. **\[Default: 1\]**

- **--final-step-size** *\<double\>*

  Initial optimizer step size in pixels. **\[Default: 0.125\]**

- **--delta-f-threshold** *\<double\>*

  Optional threshold to terminate optimization (level) if relative change of target function drops below this value. **\[Default: 0\]**

- **--crop-reference-from-index** *\<string\>*

  Crop reference image from index x,y,z. **\[Default: NONE\]**

- **--crop-reference-to-index** *\<string\>*

  Crop reference image to index x,y,z. **\[Default: NONE\]**

## 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.