mcwarp - Multi-channel nonrigid registration

       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 3.3.1p2                                       Feb 26 2025                                         mcwarp(1)

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

       Report bugs at http://nitrc.org/projects/cmtk/

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

http://www.fsf.org/licensing/licenses/gpl.html

       mcwarp - Multi-channel nonrigid registration

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   MainOptions--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.  [Thisisthedefault]--covariance, -C
            Use covariance matrix determinants to compute entropies.

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

       --mi Use standard mutual information metric [default] [Thisisthedefault]--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]

       mcwarp [options] mcaffineOutput