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

--max-stepsize <double>

Maximum optimizer step size, which determines search space exploration. [Default: 8]

--min-stepsize <double>

Minimum optimizer step size, which determines precision. [Default: 0.1]

--stepfactor <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. This can be 3 (translation), 6 (rigid: translation and rotation), 7 (rigid plus global scale), 9 (rigid plus anisotropic scales), 12 (rigid plus scales plus shears), 3003 (translation plus shear), 3033 (translation, shear, and scale) or 3303 (rigid plus shears, but no scale). This option can be repeated, in which case DOFs are used for successive optimization runs in the order that they appear.

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

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

--symmetric

Use symmetric registration functional to simultaneously estimate forward and inverse transformation. This increases ragistration time substantially but produces a result that is invariant under exchange of fixed and moving image. It may also be more robust and/or more accurate than forward-only registration.

--restrict-in-plane

Restrict the affine transformation to be in-plane for planes perpendicular to a given coordinate axis. Supported values: "xy", "xz", "yz", "none", where the default is "none", or use one of the following:

--init

Select initializer for the affine trasnformation. Supported values: "none", "fov", "com", "pax", "physical", where the default is "fov", or use one of the following:

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

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:

--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

--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

--output <string>, -o <string>

Output path for final transformation [Default: NONE]

--write-matrix <string>

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

--write-parameters <string>

Output path for final transformation in plain parameter list format [Default: NONE]

--write-protocol <string>

Optimization protocol output file name [Default: NONE]

--write-time <string>

Computation time statistics output file name [Default: NONE]

Import Results into Slicer

--write-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]