cmtk-groupwise_affine: Affine population registration

OPTIONS

--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).

--rmi: Use the RMI (a.k.a. regional mutual information) metric to drive the registration).
--congeal: Use the congealing algorithm using pixelwise stack entropies to drive the registration. [This is the default]

--template <string>, -t <string>: Input filename for pre-defined template image. [Default: NONE]
--template-with-data <string>, -T <string>: Use user-supplied template images's pixel data in registration [Default: disabled]

--output-root <string>, -O <string>: Root directory for all output files. [Default: NONE]
--output <string>, -o <string>: Output filename for groupwise registration archive. [Default: groupwise.xforms ]
--output-average <string>: Output filename for registered average image. [Default: average.nii ]
--average-linear: Use linear interpolation for average image [This is the default]
--average-cubic: Use cubic interpolation for average image
--no-output-average: Do not write average image.

--downsample-from <integer>, -d <integer>: Initial downsampling factor [Default: 4]
--downsample-to <integer>, -D <integer>: Final downsampling factor. [Default: 1]
--sampling-density <float>, -s <float>: Probabilistic sampling density. Legal values between 0 and 1. [Default: disabled]

--force-background <integer>, -B <integer>: Force background pixels (outside FOV) to given (bin) value. [Default: disabled]
--histogram-bins <integer>, -H <integer>: Manually set number of histogram bins for entropy evaluation [Default: disabled]
--crop-histograms: Crop image histograms to make better use of histogram bins.
--smooth <double>: Sigma of Gaussian smoothing kernel in multiples of template image pixel size. [Default: disabled]
--match-histograms: Match all image histograms to template data (or first image, if no template image is given)
--free-and-reread: Free memory allocated for original image whenever these are not needed and re-read image files as needed. This can be useful when running on a machine with limited memory resources.

--dofs <integer>[,<integer>,...]: Add DOFs to list [default: one pass, 6 DOF]
--zero-sum, -z: Enforce zero-sum computation.
--normal-group-first-n <integer>, -N <integer>: First N images are from the normal group and should be registered unbiased. [Default: 0]
--zero-sum-first-n <integer>, -Z <integer>: Enforce zero-sum computation for first N images. [Default: disabled]

--align-bounding-boxes: Initially align centers of bounding boxes of all images by translations [This is the default]
--align-centers-of-mass: Initially align centers of mass by translations
--init-scales: Initialize scale factors using first-order moments

--exploration <double>, -e <double>: Exploration of optimization in pixels [Default: 0.25]
--accuracy <double>, -a <double>: Accuracy of optimization in pixels [Default: 0.01]
--repeat-level <integer>, -r <integer>: Number of repetitions per optimization level [Default: 5]
--step-factor <double>, -S <double>: Step factor for successive optimization passes [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]
--disable-optimization: Disable optimization and output initial configuration.