Provided by: cmtk_3.3.1-1.2build1_amd64

**NAME**

unwarp_image_phantom - Create transformation to unwarp an image based on a phantom description

**SYNOPSIS**

unwarp_image_phantomInputPhantom 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**

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--helpWrite list of basic command line options to standard output.--help-allWrite complete list of basic and advanced command line options to standard output.--wikiWrite list of command line options to standard output in MediaWiki markup.--manWrite man page source in 'nroff' markup to standard output.--versionWrite toolkit version to standard output.--echoWrite the current command line to standard output.--verbose-level<integer>Set verbosity level.--verbose,-vIncrement verbosity level by 1 (deprecated; supported for backward compatibility).--threads<integer>Set maximum number of parallel threads (for POSIX threads and OpenMP).FittingOptions--fit-inverseFit 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-forwardFit forward transformation (mapping expected to actual landmark locations). This is useful for rectifying the image via reslicing (using 'reformatx').[Thisisthedefault]TransformationModels--splineFit B-spline free-form deformation.--polyFit polynomial transformation.[Thisisthedefault]PolynomialFittingOptions(with--poly)--degree<integer>Degree of the fitted polynomial transformation.[Default:4]B-SplineFittingOptions(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-affineDisable 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.