NAME¶
unwarp_image_phantom - Create transformation to unwarp an image based on a
phantom description
SYNOPSIS¶
unwarp_image_phantom InputPhantom InputImage OutputXform
DESCRIPTION¶
This tool computes either a polynomial transformation or 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¶
- --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 (mapping actual to expected landmark
locations). This is useful for computing a Jacobian volume correction map
(using 'reformatx') without having to numerically invert the fitted
unwarping transformation.
- --fit-forward
- Fit forward transformation (mapping expected to actual landmark
locations). This is useful for rectifying the image via reslicing (using
'reformatx'). [This is the default]
- --spline
- Fit B-spline free-form deformation.
- --poly
- Fit polynomial transformation. [This is the default]
Polynomial Fitting Options (with --poly)¶
- --degree <integer>
- Degree of the fitted polynomial transformation. [Default: 4]
B-Spline Fitting Options (with --spline)¶
- --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]
- --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.
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.