NAME

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

SYNOPSIS

       unwarp_image_phantom InputPhantom InputImage OutputXform

DESCRIPTION

       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.

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  -  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]

       --no-fit-affine
            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]

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.