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make_initial_affine - Initialize affine transformation

make_initial_affine(1) The Computational Morphometry Toolkit make_initial_affine(1)

NAME

make_initial_affine - Initialize affine transformation

SYNOPSIS

make_initial_affine ReferenceImage FloatingImage OutputXform

DESCRIPTION

Compute initial affine transformation by aligning centers of mass or principal axes

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.
--xml
Write command line syntax specification in XML markup (for Slicer integration).
--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).

Transformation construction control

--mode
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:
--direction-vectors
Alignment based on image direction vectors [This is the default]
--centers-of-mass
Alignment based on centers of mass (translation only)
--principal-axes
Alignment based on principal axes
--identity
Create only an identity transformation
--center-xform, -C
Set transformation center (for rotation, scale) to center of reference image.
--native-space
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.

Image/Transformation Database

--db <string>
Path to image/transformation database that should be updated with the newly transformation from reference to floating image. [Default: NONE]

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.
Sep 11 2017 CMTK 3.3.1