groupwise_warp - Nonrigid population registration

       CMTK  is  developed  with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and
       Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through  September
       2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.

CMTK 3.3.1p2                                       Feb 26 2025                                 groupwise_warp(1)

       Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.  Maurer,  Daniel  B.
       Russakoff, and Yaroslav Halchenko

       Report bugs at http://nitrc.org/projects/cmtk/

       This  tool  nonrigidly  registers  a population of input images simultaneously, without a template, using
       either the 'congealing' algorithm or a groupwise similarity measure based on a  continuous  approximation
       of mutual information ('RMI').

http://www.fsf.org/licensing/licenses/gpl.html

       groupwise_warp - Nonrigid population registration

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   RegistrationMetricOptions--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.  [Thisisthedefault]TemplateImageOptions--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]MulturesolutionParameters--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]OutputOptions--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)

   ImageOptionsandOperations--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]TransformationParameters--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]TransformationConstraintOptions--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]OptimizationParameters--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.

       groupwise_warp [options] affineGroupRegistration