cmtk-warpx: B-spline nonrigid registration

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 import/export

--initial <transformation-path>: Initialize transformation from given path [Default: NONE]
--invert-initial: Invert given (affine) initial transformation.
--write-itk-xform <transformation-path>: Output path for final transformation in ITK format [Default: NONE]
--write-reformatted <image-path>: Write reformatted floating image. [Default: NONE]

Transformation parameters

--grid-spacing <double>: Control point grid spacing [Default: 10]
--grid-refine <integer>: Number of refinements (control point grid resolution levels) [Default: 0]
--delay-refine: Delay control point grid refinement; first switch to next higher image resolution
--exact-spacing: Use exact control point spacing; do not modify spacing to fit reference image bounding box
--ignore-edge <integer>: Ignore n control point layers along each image face [Default: 0]
--restrict <string>: Restrict deformation to coordinate dimension(s) [one or more of 'x','y','z'] [Default: NONE]
--no-adaptive-fix: Disable adaptive fixing of control points; optimize all deformation parameters
--adaptive-fix-thresh <float>: Threshold factor for entropy criterion to fix local control points [Default: 0.5]
--accurate: Accurate computation mode: may give slightly better results after substantially longer computation [This is the default]
--fast: Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time

Regularization parameters

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

Optimization parameters

--max-stepsize <double>: Maximum optimizer step size, which determines search space exploration. [Default: -1]
--min-stepsize <double>: Minimum optimizer step size, which determines precision. [Default: -1]
--stepfactor <double>: Factor for search step size reduction. Must be > 0.0 and < 1.0 [default: 0.5] [Default: 0.5]
--delta-f-threshold <double>: Optional threshold to terminate optimization (level) if relative change of target function drops below this value. [Default: 0]
--no-maxnorm: Use Euclid norm for gradient normalication in optimization, rather than maximum norm

Image resolution parameters

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

Image data

--registration-metric

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:

--nmi: Normalized Mutual Information metric [This is the default]
--mi: Standard Mutual Information metric
--cr: Correlation Ratio metric
--rms: Root of Mean Squaresa metric (this is the square root of MSD)
--msd: Mean Squared Difference metric
--ncc: Normalized Cross Correlation metric

Floating Image Interpolation Options

--interpolation

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: Nearest neighbor interpolation (for intensity and label data)
--linear: Trilinear interpolation
--cubic: Tricubic interpolation
--cosine-sinc: Cosine-windowed sinc interpolation (most accurate but slowest)
--partial-volume: Partial volume interpolation (for label data)
--automatic: Select interpolation automatically based on data type: linear for grey-level data, nearest neighbor for label data. [This is the default]

--match-histograms

Match floating image histogram to reference image histogram.

--repeat-match-histograms

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-outside-value <double>

Force values outside field of view to this value rather than drop incomplete pixel pairs [Default: disabled]

Reference Image Preprocessing

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

Floating Image Preprocessing

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

Output parameters

--outlist <string>, -o <string>: Output path for final transformation [Default: NONE]
--time <string>, -t <string>: Computation time statistics output file name [Default: NONE]
--output-intermediate: Write transformation for each level [default: only write final transformation]

Image/Transformation Database

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

cmtk-warpx (1)

SYNOPSIS

DESCRIPTION