make_initial_affine(1)				       The Computational Morphometry Toolkit				    make_initial_affine(1)

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, 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 					    make_initial_affine(1)