## 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## 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.