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]

--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>, -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 [This is the default]

--fast

Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time

--switch, -S

Switch reference and floating image

Regularization parameters¶

--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.

Optimization parameters¶

--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

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", "msd", "ncc", where the default is "nmi", or use one of the following:

--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]

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

--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]

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

--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]

Output parameters¶

--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/Transformation Database¶

--db <string>

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