---
name: "cmtk-groupwise_init"
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_init"
---

# cmtk-groupwise\_init(1)

Affine initialization for groupwise registration

## NAME

groupwise\_init - Affine initialization for groupwise registration

## SYNOPSIS

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

## DESCRIPTION

Compute initial affine alignment for a group of input images, which can be used as an input for groupwise registration

## 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

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

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

- **--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-cubic**

  Use cubic (rather than linear) interpolation for average image.

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

  Do not write average image.

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

  Initially align centers of mass rather than centers of bounding boxes.

- **--init-scales**

  Initialize scale factors using first-order moments

- **--center-template**

  Center aligned images in template grid field of view.

- **--outputtype**

  Scalar data type for the output average image. Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", where the default is "float", or use one of the following:

  - **--char**

    8 bits, signed

  - **--byte**

    8 bits, unsigned

  - **--short**

    16 bits, signed

  - **--ushort**

    16 bits, unsigned

  - **--int**

    32 bits signed

  - **--uint**

    32 bits unsigned

  - **--float**

    32 bits floating point **\[This is the default\]**

  - **--double**

    64 bits floating point

## 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.