This is the command cmtk-make_initial_affine that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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