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.

CMTK 3.0.0                                         Jan 15 2014                           unwarp_image_phantom(1)