DOKK / manpages / debian 10 / cmtk / cmtk-warpx.1.en
warpx(1) The Computational Morphometry Toolkit warpx(1)

warpx - B-spline nonrigid registration

warpx ReferenceImage FloatingImage InitialXform

This program performs nonrigid image registration using multi-resolution optimization of voxel-based image similarity measures and a multi-resolution B-spline transformation model.

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write command line syntax specification in XML markup (for Slicer integration).
Write toolkit version to standard output.
Write the current command line to standard output.
Set verbosity level.
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Initialize transformation from given path [Default: NONE]
Invert given (affine) initial transformation.
Output path for final transformation in ITK format [Default: NONE]
Write reformatted floating image. [Default: NONE]

Control point grid spacing [Default: 10]
Number of refinements (control point grid resolution levels) [Default: 0]
Delay control point grid refinement; first switch to next higher image resolution
Use exact control point spacing; do not modify spacing to fit reference image bounding box
Ignore n control point layers along each image face [Default: 0]
Restrict deformation to coordinate dimension(s) [one or more of 'x','y','z'] [Default: NONE]
Disable adaptive fixing of control points; optimize all deformation parameters
Threshold factor for entropy criterion to fix local control points [Default: 0.5]
Accurate computation mode: may give slightly better results after substantially longer computation [This is the default]
Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time

Weight for Jacobian-based local volume preservation constraint [Default: 0]
Weight for smoothness constraint based on second-order grid bending energy. [Default: 0]
Weight for inverse consistency constraint [Default: 0]
Weight relaxation factor for alternating under-constrained iterations [Default: -1]
Before each resolution level, regularize negative-Jacobian areas of the deformation to unfold them.

Maximum optimizer step size, which determines search space exploration. [Default: -1]
Minimum optimizer step size, which determines precision. [Default: -1]
Factor for search step size reduction. Must be > 0.0 and < 1.0 [default: 0.5] [Default: 0.5]
Optional threshold to terminate optimization (level) if relative change of target function drops below this value. [Default: 0]
Use Euclid norm for gradient normalication in optimization, rather than maximum norm

Image sampling (finest resampled image resolution) [Default: -1]
Upper limit for image sampling in multiresolution hierarchy [Default: -1]
Do not use original data in full resolution for final registration stage.

Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "rms", "msd", "ncc", where the default is "nmi", or use one of the following:
Normalized Mutual Information metric [This is the default]
Standard Mutual Information metric
Correlation Ratio metric
Root of Mean Squaresa metric (this is the square root of MSD)
Mean Squared Difference metric
Normalized Cross Correlation metric

Interpolation method for floating image sampling: Supported values: "nearest-neighbor", "linear", "cubic", "cosine-sinc", "partial-volume", "automatic", where the default is "automatic", or use one of the following:
Nearest neighbor interpolation (for intensity and label data)
Trilinear interpolation
Tricubic interpolation
Cosine-windowed sinc interpolation (most accurate but slowest)
Partial volume interpolation (for label data)
Select interpolation automatically based on data type: linear for grey-level data, nearest neighbor for label data. [This is the default]
Match floating image histogram to reference image histogram.
Repeat histogram matching after every level of the registration to account for volume changes. When registering masked data, it is advisable to also use the --force-outside-value option to prevent poorly matched histograms.
Force values outside field of view to this value rather than drop incomplete pixel pairs [Default: disabled]

Data class: grey (default) or label [Default: NONE]
Padding value [Default: disabled]
Minimum value truncation threshold [Default: disabled]
Maximum value truncation threshold [Default: disabled]
Number of bins for histogram-based pruning [Default: disabled]
Apply histogram equalization
Apply median filter with given radius [Default: 0]
Apply Sobel edge detection filter
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]
Automatic cropping based on threshold [Default: disabled]

Data class: grey (default) or label [Default: NONE]
Padding value [Default: disabled]
Minimum value truncation threshold [Default: disabled]
Maximum value truncation threshold [Default: disabled]
Number of bins for histogram-based pruning [Default: disabled]
Apply histogram equalization
Apply median filter with given radius [Default: 0]
Apply Sobel edge detection filter
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]
Automatic cropping based on threshold [Default: disabled]

Output path for final transformation [Default: NONE]
Computation time statistics output file name [Default: NONE]
Write transformation for each level [default: only write final transformation]

Path to image/transformation database that should be updated with the new registration and/or reformatted image. [Default: NONE]

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

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

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.

Jan 25 2019 CMTK 3.3.1p1