.TH groupwise_init "1" "Jan 25 2019" "CMTK 3.3.1p1" "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.
.TP 5
\fB\-\-outputtype\fR
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:
.RS 5
.TP 5
\fB\-\-char\fR
8 bits, signed
.TP 5
\fB\-\-byte\fR
8 bits, unsigned
.TP 5
\fB\-\-short\fR
16 bits, signed
.TP 5
\fB\-\-ushort\fR
16 bits, unsigned
.TP 5
\fB\-\-int\fR
32 bits signed
.TP 5
\fB\-\-uint\fR
32 bits unsigned
.TP 5
\fB\-\-float\fR
32 bits floating point
\fB[This is the default]\fR
.TP 5
\fB\-\-double\fR
64 bits floating point

.RE
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.