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.