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, 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.