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


unwarp_image_phantom InputPhantom InputImage OutputXform


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.


Global Toolkit Options (these are shared by all CMTK tools)
Write list of basic command line options to standard output.

Write complete list of basic and advanced command line options to standard output.

Write list of command line options to standard output in MediaWiki markup.

Write man page source in 'nroff' markup to standard output.

Write toolkit version to standard output.

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 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 transformation (mapping expected to actual landmark locations). This is
useful for rectifying the image via reslicing (using 'reformatx'). [This is the

Transformation Models
Fit B-spline free-form deformation.

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]

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


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

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