Provided by: cmtk_3.0.0-1ubuntu1_amd64
unwarp_image_phantom - Unwarp T1-weighted MR image using a phantom description
unwarp_image_phantom InputPhantom InputImage OutputXform
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.
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 --fit-inverse Fit inverse transformation - this is useful for computing a Jacobian volume correction map (using 'reformatx') without having to numerically invert the fitted unwarping transformation. --levels <integer> Number of levels in the multi-level B-spline approximation procedure. [Default: 1] --iterations-per-level <integer> Maximum number of spline coefficient update iterations per level in the multi-level B-spline approximation procedure. [Default: 100] --rms-threshold <double> Threshold for relative improvement of the RMS fitting residual. The fitting iteration terminates if (rmsAfterUpdate-rmsBeforeUpdate)/rmsBeforeUpdate < threshold. [Default: 0] --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]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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.