groupwise_init(1)				       The Computational Morphometry Toolkit					 groupwise_init(1)

NAME

       groupwise_init - Affine initialization for groupwise registration

SYNOPSIS

       groupwise_init [options] image0 [image1 ...]

DESCRIPTION

       Compute initial affine alignment for a group of input images, which can be used as an input for groupwise registration

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
       --template <string>, -t <string>
	    Input filename for pre-defined template image.  [Default: NONE]

       --output-root <string>, -O <string>
	    Root directory for all output files.  [Default: NONE]

       --output <string>, -o <string>
	    Output filename for groupwise registration archive.  [Default: groupwise.xforms ]

       --output-average <string>
	    Output filename for registered average image.  [Default: average.nii ]

       --average-cubic
	    Use cubic (rather than linear) interpolation for average image.

       --no-output-average
	    Do not write average image.

       --align-centers-of-mass
	    Initially align centers of mass rather than centers of bounding boxes.

       --init-scales
	    Initialize scale factors using first-order moments

       --center-template
	    Center aligned images in template grid field of view.

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 						 groupwise_init(1)