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).

Optimization

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

Accuracy (final optimization step size in [mm]. [Default: 0.1]

--sampling <double>, -s <double>

Resampled image resolution. This is the resolution [in mm] of the first (finest) resampled image in the multi-scale pyramid, which is derived directly from the original full-resolution images. [Default: 1]

--levels <integer>, -l <integer>

Number of resolution levels. The algorithm will create (levels-1) resampled images with increasingly coarse resolution and use these in successive order of increasing resolution before using the original images at the final level. [Default: 4]

--fix-offset

Fix symmetry plane offset. Reduces computation time and forces symmetry plane to cross center of mass, but may lead to less-than-accurate result.

Initial approximate symmetry plane orientation

--initial-plane

Initial orientation of symmetry plane. This should be the closest orthogonal plane to the expected actual symmetry plane. Supported values: "initial-axial", "initial-coronal", "initial-sagittal", "initial-xy", "initial-xz", "initial-yz", where the default is "initial-sagittal", or use one of the following:

Pre-computed symmetry

--output-only <string>

Give symmetry parameters [Rho Theta Phi] as option, skip search. [Default: disabled]

--output-only-file <string>

Read symmetry parameters from file, skip search. [Default: disabled]

Data pre-processing

--min-value <float>

Force minumum data value. [Default: disabled]

--max-value <float>

Force maximum data value. [Default: disabled]

Output of Images

--interpolation

Interpolation method used for reformatted output data Supported values: "linear", "cubic", "sinc", where the default is "linear", or use one of the following:

--pad-out <double>, -P <double>

Padding value for output images. [Default: disabled]

--mark-value <double>

Data value to mark (draw) symmetry plane. [Default: 4095]

--write-marked <image-path>

File name for output image with marked symmetry plane. [Default: NONE]

--write-aligned <image-path>

File name for symmetry plane-aligned output image. [Default: NONE]

--mark-aligned

Mark symmetry plane in aligned output image.

--write-subtract <image-path>

File name for mirror subtraction image. [Default: NONE]

--write-mirror <image-path>

File name for image mirrored w.r.t. symmetry plane. [Default: NONE]

Output of Parameters

--outfile <path>, -o <path>

File name for symmetry plane parameter output. [Default: NONE]

--write-xform <transformation-path>

Write affine alignment transformation to file [Default: NONE]