cmtk-groupwise_warp: Nonrigid 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>: Override template image with given file. [Default: NONE]
--template-with-data <string>, -T <string>: Use user-supplied template images's pixel data in registration [Default: disabled]

--downsample-from <integer>, -d <integer>: Initial downsampling factor [4]. [Default: 4]
--downsample-to <integer>, -D <integer>: Final downsampling factor [1]. [Default: 1]
--sampling-density <float>, -s <float>: Probabilistic sampling density [default: off]. [Default: -1]

--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 ]
--no-output-average: Do not write average image.
--average-cubic: Use cubic interpolation for average image (default: linear)

--force-background <integer>, -B <integer>: Force background pixels (outside FOV) to given (bin) value. [Default: disabled]
--histogram-bins <integer>, -H <integer>: Set number of histogram bins for entropy evaluation. [Default: disabled]
--crop-histograms: Crop image histograms to make better use of histogram bins.
--match-histograms: Match all image histograms to template data (or first image, if no template image is given)
--repeat-match-histograms: Frequetly repeat histogram-based intensity matching to account for changing volume proportions.
--smooth-pixels <double>: Sigma of Gaussian smoothing kernel in multiples of template image pixel size [Default: disabled]
--smooth-cps <double>: Sigma of Gaussian smoothing kernel in multiples of control point delta [Default: disabled]

--grid-spacing <double>: Control point grid spacing. [Default: 40]
--grid-spacing-fit: Use grid spacing that fits volume FOV
--refine-grid <integer>, -r <integer>: Number of times to refine transformation grid [default: 0]. [Default: 0]

--zero-sum, -z: Enforce zero-sum computation.
--zero-sum-no-affine: Enforce zero-sum computation EXCLUDING affine components.
--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]
--jacobian-weight <float>, -J <float>: Weight for Jacobian volume preservation constraint [default: off] [Default: 0]
--bending-energy-weight <float>, -E <float>: Weight for grid bending energy regularization constraint [default: off] [Default: 0]

--exploration <double>, -e <double>: Exploration of optimization in pixels [Default: 0.25]
--accuracy <double>, -a <double>: Accuracy of optimization in pixels [Default: 0.01]
--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]
--partial-gradient-thresh <float>, -p <float>: Threshold factor for partial gradient zeroing [<0 turn off] [Default: 0]
--activate-uninformative: Activate potentially uninformative control points
--disable-cp-mask <string>: Path to mask image (matching template grid) defining areas in which control points should be disabled. This guarantees that mask foreground areas remain undeformed. [Default: NONE]
--disable-optimization: Disable optimization and output initial configuration.