---
name: "cmtk-make_initial_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-make_initial_affine"
---

# cmtk-make\_initial\_affine(1)

Initialize affine transformation

## NAME

make\_initial\_affine - Initialize affine transformation

## SYNOPSIS

**make\_initial\_affine** ReferenceImage FloatingImage OutputXform

## DESCRIPTION

Compute initial affine transformation by aligning centers of mass or principal axes

## 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).

### Transformation construction control

- **--mode**

  Mode selection for initialization Supported values: "direction-vectors", "centers-of-mass", "principal-axes", "identity", where the default is "direction-vectors", or use one of the following:

  - **--direction-vectors**

    Alignment based on image direction vectors **\[This is the default\]**

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

    Alignment based on centers of mass (translation only)

  - **--principal-axes**

    Alignment based on principal axes

  - **--identity**

    Create only an identity transformation

- **--center-xform**, **-C**

  Set transformation center (for rotation, scale) to center of reference image.

- **--native-space**

  Write transformation between the native image spaces, rather than in CMTK standard RAS space. This is the default when running this tool as a Slicer plugin.

### Image/Transformation Database

- **--db** *\<string\>*

  Path to image/transformation database that should be updated with the newly transformation from reference to floating image. **\[Default: NONE\]**

## 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.