mcaffine - Multi-channel affine 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                                       mcaffine(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 affine image registration using histogram-based or covariance-based joint entropy measures

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

       mcaffine - Multi-channel affine 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]--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] [Thisisthedefault]--mi Use standard mutual information metric

       --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]

       --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]

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