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

# cmtk-unwarp\_image\_phantom(1)

Create transformation to unwarp an image based on a phantom description

## NAME

unwarp\_image\_phantom - Create transformation to unwarp an image based on a phantom description

## SYNOPSIS

**unwarp\_image\_phantom** InputPhantom InputImage OutputXform

## DESCRIPTION

This tool computes either a polynomial transformation or B-spline free-form deformation to unwarp an image. The transformation is based on expected and detected landmarks in an image of a structural phantom acquired on the same scanner. Use the 'detect\_adni\_phantom' tool to detect landmarks of the ADNI Phantom in an image and generate a phantom description file suitable for use with this tool.

## 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).

### Fitting Options

- **--fit-inverse**

  Fit inverse transformation (mapping actual to expected landmark locations). This is useful for computing a Jacobian volume correction map (using 'reformatx') without having to numerically invert the fitted unwarping transformation.

- **--fit-forward**

  Fit forward transformation (mapping expected to actual landmark locations). This is useful for rectifying the image via reslicing (using 'reformatx'). **\[This is the default\]**

### Transformation Models

- **--spline**

  Fit B-spline free-form deformation.

- **--poly**

  Fit polynomial transformation. **\[This is the default\]**

### Polynomial Fitting Options (with --poly)

- **--degree** *\<integer\>*

  Degree of the fitted polynomial transformation. **\[Default: 4\]**

### B-Spline Fitting Options (with --spline)

- **--final-cp-spacing** *\<double\>*

  Final control point grid spacing of the output B-spline transformation. **\[Default: 0\]**

- **--final-cp-dims** *\<string\>*

  Final control point grid dimensions (i.e., number of control points) of the output B-spline transformation. To be provided as 'dimX,dimY,dimZ'. **\[Default: NONE\]**

- **--levels** *\<integer\>*

  Number of levels in the multi-level B-spline approximation procedure. **\[Default: 1\]**

- **--iterations-per-level** *\<integer\>*

  Maximum number of spline coefficient update iterations per level in the multi-level B-spline approximation procedure. **\[Default: 100\]**

- **--rms-threshold** *\<double\>*

  Threshold for relative improvement of the RMS fitting residual. The fitting iteration terminates if (rmsAfterUpdate-rmsBeforeUpdate)/rmsBeforeUpdate \< threshold. **\[Default: 0\]**

- **--no-fit-affine**

  Disable fitting of affine transformation to initialize spline. Instead, fit spline directly. This usually gives worse results and is discouraged.

## 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.