mcwarp(1)					       The Computational Morphometry Toolkit						 mcwarp(1)

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, and Daniel B. Russakoff

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From  April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 							 mcwarp(1)