NAME¶

unwarp_image_phantom - Unwarp T1-weighted MR image using a phantom description

SYNOPSIS¶

unwarp_image_phantom InputPhantom InputImage OutputXform

DESCRIPTION¶

This tool computes a B-spline free-form deformation to unwarp an image. The transformation is based on expected and detected landmarks in an image of a structural phantom acquired on the same scanner. Use the 'detect_adni_phantom' tool to detect landmarks of the ADNI Phantom in an image and generate a phantom description file suitable for use with this tool.

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.

--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).

Fitting Options¶

--levels <integer>

Number of levels in the multi-level B-spline approximation procedure. [Default: 1]

--no-fit-affine

Disable fitting of affine transformation to initialize spline. Instead, fit spline directly. This usually gives worse results and is discouraged.

Output Options¶

--final-cp-spacing <double>

Final control point grid spacing of the output B-spline transformation. [Default: 0]

--final-cp-dims <string>

Final control point grid dimensions (i.e., number of control points) of the output B-spline transformation. To be provided as 'dimX,dimY,dimZ'. [Default: NONE]

AUTHORS¶

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff

LICENSE¶

http://www.fsf.org/licensing/licenses/gpl.html

BUGS¶

Report bugs at http://nitrc.org/projects/cmtk/

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).