cmtk-registration: Rigid and affine registration

OPTIONS

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:

--nmi: Normalized Mutual Information metric [This is the default]
--mi: Standard Mutual Information metric
--cr: Correlation Ratio metric
--msd: Mean Squared Difference metric
--ncc: Normalized Cross Correlation metric

--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]

cmtk-registration (1)

SYNOPSIS

DESCRIPTION