GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).
Transformationimport/export--initial<transformation-path>
Initialize transformation from given path [Default:NONE]--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]Transformationparameters--grid-spacing<double>, -g<double>
Control point grid spacing [Default:15]--exact-spacing
Use exact control point spacing; do not modify spacing to fit reference image bounding box
--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
--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
[Thisisthedefault]--fast
Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU
time
--switch, -S
Switch reference and floating image
Regularizationparameters--jacobian-weight<float>
Weight for Jacobian-based local volume preservation constraint [Default:0]--energy-weight<float>
Weight for grid bending energy constraint [Default:0]--rigidity-weight<float>
Weight for local rigidity constraint [Default:0]--ic-weight<float>
Weight for inverse consistency constraint [Default:0]--relax<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.
Optimizationparameters--exploration<double>, -e<double>
Search space exploration (initial step size) [Default:-1]--accuracy<double>, -a<double>
Search accuracy (initial step size) [Default:-1]--stepfactor<double>, -f<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
Imageresolutionparameters--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.
Imagedata--registration-metric
Registration metric for motion estimation by image-to-image registration. Supported values: "nmi",
"mi", "cr", "msd", "ncc", where the default is "nmi", or use one of the following:
--nmi
Normalized Mutual Information metric [Thisisthedefault]--mi Standard Mutual Information metric
--cr Correlation Ratio metric
--msd
Mean Squared Difference metric
--ncc
Normalized Cross Correlation metric
--match-histograms
Match floating image histogram to reference image histogram.
--force-outside-value<double>
Force values outside field of view to this value rather than drop incomplete pixel pairs [Default:disabled]ReferenceImagePreprocessing--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
--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]FloatingImagePreprocessing--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
--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]Outputparameters--outlist<string>, -o<string>
Output path for final transformation [Default:NONE]--protocol<string>, -p<string>
Optimization protocol output file name [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/TransformationDatabase--db<string>
Path to image/transformation database that should be updated with the new registration and/or
reformatted image. [Default:NONE]
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