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.

--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

--exclude-first-image, -x

Exclude first image from reconstruction as a separate registration target image)

--crop <string>

Crop reference to pixel region x0,y0,z1:x1,y1,z1

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

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

Reconstruction Grid

--recon-grid <string>

Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)

--recon-grid-path <string>, -R <string>

Give path to grid that defines reconstructed image grid [including offset] [Default: NONE]

Initial Volume Injection Parameters

--isotropic-injection

Use isotropic volume injection [otherwise: scaled with pass image pixel size per dimension]

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

Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 1]

--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]

Volume Reconstruction 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:

--deblurring

Kernel shape to approximate the point spread function for joint deblurring reconstruction (selecting one of these disables inverse interpolation reconstruction) Supported values: "box", "gaussian", or use one of the following:

--psf <string>

Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel reconstrunction.

--psf-scale <double>

Scale point spread function size by this value. Use with 'deblurring' kernel reconstrunction. [Default: 1]

Optimization Parameters

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

Maximum number of inverse interpolation iterations [Default: 20]

--fourth-order-error, -f

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

Regularization Parameters

--l-norm-weight <double>

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

--no-truncation, -T

Turn off non-linear regional intensity truncation

Output Options

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

Output path for final reconstructed image [Default: reconstructed.nii ]

--write-injected-image <string>

Write initial volume-injected image to this path [Default: NONE]

--write-lowest-max-error-image <string>

Optional path to write reconstructed image with lowest MAXIMUM error. [Default: NONE]

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

Write output images as floating point