cmtk-mcaffine(1) [debian man page]

mcaffine(1)					       The Computational Morphometry Toolkit					       mcaffine(1)

NAME

       mcaffine - Multi-channel affine registration

SYNOPSIS

       mcaffine [options] refChannel0 [refChannel1 ...] -- fltChannel0 [fltChannel1 ...]

DESCRIPTION

       Multi-channel affine 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]

       --initial-xform <string>
	    Optional path of a file with the initial transformation.  [Default: NONE]

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

       --downsample-to <integer>, -D <integer>
	    Final downsampling factor [1]. Factor 0 is full resolution with smoothing turned off [Default: 1]

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

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

       --dofs <integer>[,<integer>,...]
	    Set sequence of numbers of DOFs for optimization schedule [can be repeated]. Supported values are: 0, 3, 6, 7, 9, 12.

       --nmi
	    Use normalized mutual information metric [default] [This is the default]

       --mi Use standard mutual information metric

       --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]

       --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]

       --crop-reference-from-index <string>
	    Crop reference image from index x,y,z.  [Default: NONE]

       --crop-reference-to-index <string>
	    Crop reference image to index x,y,z.  [Default: NONE]

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 						       mcaffine(1)