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).

Input Options¶

--padding-value <double>

Set padding value for input image. Pixels with this value will be ignored. [Default: disabled]

Interleaving Options¶

--interleave-axis

Define interleave axis: this is the through-slice direction of the acquisition. Supported values: "guess-from-input", "axial", "sagittal", "coronal", "interleave-x", "interleave-y", "interleave-z", where the default is "guess-from-input", or use one of the following:

--passes <integer>, -p <integer>

Number of interleaved passes [Default: 2]

--pass-weight <string>, -W <string>

Set contribution weight for a pass in the form 'pass:weight'

Motion Correction / Registration Options¶

--reference-image <image-path>, -R <image-path>

Use a separate high-resolution reference image for registration [Default: NONE]

--registration-metric

Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "msd", "cc", where the default is "msd", or use one of the following:

--import-xforms-path <path>

Path of file from which to import transformations between passes. [Default: NONE]

--export-xforms-path <path>

Path of file to which to export transformations between passes. [Default: NONE]

Initial Volume Injection Options¶

--injection-kernel-sigma <double>, -S <double>

Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 0.5]

--injection-kernel-radius <double>, -r <double>

Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation. [Default: 2]

Inverse Interpolation Options¶

--inverse-interpolation-kernel

Kernel for the inverse interpolation reconstruction Supported values: "cubic", "linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one of the following:

--fourth-order-error, -f

Use fourth-order (rather than second-order) error for optimization.

--num-iterations <integer>, -n <integer>

Maximum number of inverse interpolation iterations [Default: 20]

Reconstruction Regularization Options¶

--l-norm-weight <double>

Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) [Default: 0]

--no-truncation, -T

Turn off regional intensity truncatrion

Output Options¶

--write-injected-image <image-path>

Write initial volume injection image to path [Default: NONE]

--write-images-as-float, -F

Write output images as floating point [default: same as input]