.TH groupwise_init "1" "Jul 20 2012" "CMTK 2.2.2" "The Computational Morphometry Toolkit"
.SH NAME
groupwise_init \- Affine initialization for groupwise registration
.SH SYNOPSIS
groupwise_init [options] image0 [image1 ...]
.SH DESCRIPTION
Compute initial affine alignment for a group of input images, which can be used as an input for groupwise registration
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Main Options
.TP 5
\fB\-\-template\fR \fI<string>\fR, \fB\-t\fR \fI<string>\fR
Input filename for pre-defined template image.
.B [Default: NONE]
.TP 5
\fB\-\-output-root\fR \fI<string>\fR, \fB\-O\fR \fI<string>\fR
Root directory for all output files.
.B [Default: NONE]
.TP 5
\fB\-\-output\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output filename for groupwise registration archive.
.B [Default: "groupwise.xforms"]
.TP 5
\fB\-\-output-average\fR \fI<string>\fR
Output filename for registered average image.
.B [Default: "average.nii"]
.TP 5
\fB\-\-average-cubic\fR
Use cubic (rather than linear) interpolation for average image.
.TP 5
\fB\-\-no-output-average\fR
Do not write average image.
.TP 5
\fB\-\-align-centers-of-mass\fR
Initially align centers of mass rather than centers of bounding boxes.
.TP 5
\fB\-\-init-scales\fR
Initialize scale factors using first-order moments
.TP 5
\fB\-\-center-template\fR
Center aligned images in template grid field of view.
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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).