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.