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, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

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.