Provided by: cmtk_3.0.0-1ubuntu1_amd64 bug


       unwarp_image_phantom - Unwarp T1-weighted MR image using a phantom description


       unwarp_image_phantom InputPhantom InputImage OutputXform


       This   tool   computes   a   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  -  this  is  useful  for  computing  a  Jacobian volume
            correction map (using 'reformatx') without having to numerically  invert  the  fitted
            unwarping transformation.

       --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.

   Output Options
       --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]


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



       Report bugs at


       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.