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

       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.

CMTK 3.3.1p2                                       Feb 26 2025                           unwarp_image_phantom(1)

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

       Report bugs at http://nitrc.org/projects/cmtk/

       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.

http://www.fsf.org/licensing/licenses/gpl.html

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

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   FittingOptions--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').  [Thisisthedefault]TransformationModels--spline
            Fit B-spline free-form deformation.

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

unwarp_image_phantom InputPhantom InputImage OutputXform