NAME

       mcwarp - Multi-channel nonrigid registration

SYNOPSIS

       mcwarp [options] mcaffineOutput

DESCRIPTION

       Multi-channel  nonrigid  B-spline  image registration using histogram-based or covariance-
       based joint entropy measures

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).

   Main Options
       --out-archive <string>, -o <string>
            Output archive path.  [Default: NONE]

       --downsample-from <integer>, -d <integer>
            Initial downsampling factor [1].  [Default: 1]

       --downsample-to <integer>, -D <integer>
            Final downsampling factor [1].  [Default: 1]

       --downsample-average <boolean>
            Downsample using sliding-window averaging [default: off] ) [Default: 0]

       --smooth <float>
            Sigma of Gaussian  smoothing  kernel  in  multiples  of  template  image  pixel  size
            [default: off] ) [Default: 0]

       --grid-spacing <double>
            Initial control point grid spacing in mm.  [Default: 40]

       --grid-spacing-exact <double>
            Exact initial grid spacing, even if it doesn't match image FOV.  [Default: disabled]

       --refine-grid <integer>
            Number of control point grid refinements.  [Default: 0]

       --delay-refine-grid
            Delay control point grid refinement until after pixel refinement.

       --adaptive-fix-thresh-factor <float>
            Intensity  threshold  factor  [0..1] for adaptive parameter fixing. [default: 0 -- no
            fixing] [Default: 0]

       --adaptive-fix-thresh-factor-entropy <float>
            Entropy threshold factor [0..1] for adaptive parameter  fixing.  [default:  0  --  no
            fixing] [Default: disabled]

       --fix-warp-x
            Fix transformation (do not warp) in x-direction.

       --fix-warp-y
            Fix transformation (do not warp) in y-direction.

       --fix-warp-z
            Fix transformation (do not warp) in z-direction.

       --jacobian-constraint-weight <float>
            Weight for Jacobian volume preservation constraint [Default: 0]

       --histograms, -H
            Use  multi-dimensional  histograms  to  compute  entropies  [default.   [This  is the
            default]

       --covariance, -C
            Use covariance matrix determinants to compute entropies.

       --cubic, -c
            Use cubic interpolation [default: linear]

       --mi Use standard mutual information metric [default] [This is the default]

       --nmi
            Use normalized mutual information metric

       --intensity-correction, -I
            Correct image intensities using  local  transformation  Jacobian  to  preserve  total
            signal

       --initial-step-size <double>
            Initial optimizer step size in pixels.  [Default: 1]

       --final-step-size <double>
            Initial optimizer step size in pixels.  [Default: 0.125]

       --delta-f-threshold <double>
            Optional  threshold  to  terminate  optimization (level) if relative change of target
            function drops below this value.  [Default: 0]

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.