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).

Automation Options¶

--auto-multi-levels <integer>

Automatic optimization and resolution parameter generation for <n> levels [Default: 0]

Optimization settings¶

--exploration <double>, -e <double>

Exploration [initial optimizer step size] [Default: 8]

--accuracy <double>, -a <double>

Accuracy [final optimizer step size] [Default: 0.1]

--stepfactor <double>, -f <double>

Factor for search step size reduction. Must be > 0.0 and < 1.0 [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]

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, omit final stage in multiresolution hierarchy, thus reducing computation time.

Transformation parameters¶

--dofs <integer>[,<integer>,...]

Add number of degrees of freedom [can be repeated]

--dofs-final <integer>[,<integer>,...]

Add number of degrees of freedom for final level only [can be repeated]

--no-switch, -n

Do not auto-switch reference and floating image for improved computational performance

--initxlate, -i

Initialized transformation by translating floating image FOV center onto reference image FOV center

--initial <transformation-path>

Initialize transformation from given path [Default: NONE]

--initial-is-inverse

Invert initial transformation before initializing registration

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.

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]

--out-matrix <string>

Output path for final transformation in matrix format [Default: NONE]

--out-parameters <string>

Output path for final transformation in plain parameter list format [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]

Import Results into Slicer¶

--out-itk <transformation-path>

Output path for final transformation in ITK format [Default: NONE]

--write-reformatted <image-path>

Write reformatted floating image. [Default: NONE]

Image/Transformation Database¶

--db <string>

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