.TH make_initial_affine "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
make_initial_affine \- Initialize affine transformation
.SH SYNOPSIS
\fBmake_initial_affine\fR ReferenceImage FloatingImage OutputXform 
.SH DESCRIPTION
Compute initial affine transformation by aligning centers of mass or principal axes
.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\-\-xml\fR
Write command line syntax specification in XML markup (for Slicer integration).
.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 Transformation construction control
.TP 5
\fB\-\-mode\fR
Mode selection for initialization
Supported values: "direction-vectors", "centers-of-mass", "principal-axes", "identity", where the default is "direction-vectors", or use one of the following:
.RS 5
.TP 5
\fB\-\-direction-vectors\fR
Alignment based on image direction vectors
\fB[This is the default]\fR
.TP 5
\fB\-\-centers-of-mass\fR
Alignment based on centers of mass (translation only)
.TP 5
\fB\-\-principal-axes\fR
Alignment based on principal axes
.TP 5
\fB\-\-identity\fR
Create only an identity transformation
.RE
.TP 5
\fB\-\-center-xform\fR, \fB\-C\fR
Set transformation center (for rotation, scale) to center of reference image.
.TP 5
\fB\-\-native-space\fR
Write transformation between the native image spaces, rather than in CMTK standard RAS space. This is the default when running this tool as a Slicer plugin.
.SS Image/Transformation Database
.TP 5
\fB\-\-db\fR \fI<string>\fR
Path to image/transformation database that should be updated with the newly transformation from reference to floating image.
.B [Default: NONE]
.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.