NAME

       make_initial_affine - Initialize affine transformation

SYNOPSIS

       make_initial_affine ReferenceImage FloatingImage OutputXform

DESCRIPTION

       Compute initial affine transformation by aligning centers of mass or principal axes

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.

       --xml
            Write command line syntax specification in XML markup (for Slicer integration).

       --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).

   Transformation construction control
       --mode
            Mode selection for initialization Supported values: "direction-vectors", "centers-of-
            mass", "principal-axes", "identity", where the default is "direction-vectors", or use
            one of the following:

            --direction-vectors
                 Alignment based on image direction vectors [This is the default]

            --centers-of-mass
                 Alignment based on centers of mass (translation only)

            --principal-axes
                 Alignment based on principal axes

            --identity
                 Create only an identity transformation

       --center-xform, -C
            Set transformation center (for rotation, scale) to center of reference image.

       --native-space
            Write  transformation  between  the native image spaces, rather than in CMTK standard
            RAS space. This is the default when running this tool as a Slicer plugin.

   Image/Transformation Database
       --db <string>
            Path  to  image/transformation  database  that  should  be  updated  with  the  newly
            transformation from reference to floating image.  [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.