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

# cmtk-groupwise\_affine(1)

Affine population registration

## NAME

groupwise\_affine - Affine population registration

## SYNOPSIS

groupwise\_affine \[options\] image0 \[image1 ...\]

## DESCRIPTION

This tool registers a population of input images simultaneously, without a template, using either the 'congealing' algorithm or a groupwise similarity measure based on a continuous approximation of mutual information ('RMI').

## 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).

### Registration Metric Options

- **--rmi**

  Use the RMI (a.k.a. regional mutual information) metric to drive the registration).

- **--congeal**

  Use the congealing algorithm using pixelwise stack entropies to drive the registration. **\[This is the default\]**

### Template Image Options

- **--template** *\<string\>*, **-t** *\<string\>*

  Input filename for pre-defined template image. **\[Default: NONE\]**

- **--template-with-data** *\<string\>*, **-T** *\<string\>*

  Use user-supplied template images's pixel data in registration **\[Default: disabled\]**

### Output Options

- **--output-root** *\<string\>*, **-O** *\<string\>*

  Root directory for all output files. **\[Default: NONE\]**

- **--output** *\<string\>*, **-o** *\<string\>*

  Output filename for groupwise registration archive. **\[Default: groupwise.xforms \]**

- **--output-average** *\<string\>*

  Output filename for registered average image. **\[Default: average.nii \]**

- **--average-linear**

  Use linear interpolation for average image **\[This is the default\]**

- **--average-cubic**

  Use cubic interpolation for average image

- **--no-output-average**

  Do not write average image.

### Multiresolution Parameters

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

  Initial downsampling factor **\[Default: 4\]**

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

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

- **--sampling-density** *\<float\>*, **-s** *\<float\>*

  Probabilistic sampling density. Legal values between 0 and 1. **\[Default: disabled\]**

### Image Options and Operations

- **--force-background** *\<integer\>*, **-B** *\<integer\>*

  Force background pixels (outside FOV) to given (bin) value. **\[Default: disabled\]**

- **--histogram-bins** *\<integer\>*, **-H** *\<integer\>*

  Manually set number of histogram bins for entropy evaluation **\[Default: disabled\]**

- **--crop-histograms**

  Crop image histograms to make better use of histogram bins.

- **--smooth** *\<double\>*

  Sigma of Gaussian smoothing kernel in multiples of template image pixel size. **\[Default: disabled\]**

- **--match-histograms**

  Match all image histograms to template data (or first image, if no template image is given)

- **--free-and-reread**

  Free memory allocated for original image whenever these are not needed and re-read image files as needed. This can be useful when running on a machine with limited memory resources.

### Transformation Parameters

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

  Add DOFs to list \[default: one pass, 6 DOF\]

- **--zero-sum**, **-z**

  Enforce zero-sum computation.

- **--normal-group-first-n** *\<integer\>*, **-N** *\<integer\>*

  First N images are from the normal group and should be registered unbiased. **\[Default: 0\]**

- **--zero-sum-first-n** *\<integer\>*, **-Z** *\<integer\>*

  Enforce zero-sum computation for first N images. **\[Default: disabled\]**

### Transformation Initialization

- **--align-bounding-boxes**

  Initially align centers of bounding boxes of all images by translations **\[This is the default\]**

- **--align-centers-of-mass**

  Initially align centers of mass by translations

- **--init-scales**

  Initialize scale factors using first-order moments

### Optimization Parameters

- **--exploration** *\<double\>*, **-e** *\<double\>*

  Exploration of optimization in pixels **\[Default: 0.25\]**

- **--accuracy** *\<double\>*, **-a** *\<double\>*

  Accuracy of optimization in pixels **\[Default: 0.01\]**

- **--repeat-level** *\<integer\>*, **-r** *\<integer\>*

  Number of repetitions per optimization level **\[Default: 5\]**

- **--step-factor** *\<double\>*, **-S** *\<double\>*

  Step factor for successive optimization passes **\[Default: 0.5\]**

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

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

- **--disable-optimization**

  Disable optimization and output initial configuration.

## 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.