Provided by: cmtk_3.2.2-1.4_amd64 bug


       mcaffine - Multi-channel affine registration


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


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


   Global Toolkit Options (these are shared by all CMTK tools)
            Write list of basic command line options to standard output.

            Write complete list of basic and advanced command line options to standard output.

            Write list of command line options to standard output in MediaWiki markup.

            Write man page source in 'nroff' markup to standard output.

            Write toolkit version to standard output.

            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.

            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]


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



       Report bugs at


       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.