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.

       --outputtype
            Scalar data type for the output average image.  Supported values: "char", "byte", "short", "ushort",
            "int", "uint", "float", "double", where the default is "float", or use one of the following:

            --char
                 8 bits, signed

            --byte
                 8 bits, unsigned

            --short
                 16 bits, signed

            --ushort
                 16 bits, unsigned

            --int
                 32 bits signed

            --uint
                 32 bits unsigned

            --float
                 32 bits floating point [This is the default]

            --double
                 64 bits floating point

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.