groupwise_affine - Affine 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_affine(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  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_affine - Affine 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>
            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]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]--average-linear
            Use linear interpolation for average image [Thisisthedefault]--average-cubic
            Use cubic interpolation for average image

       --no-output-average
            Do not write average image.

   MultiresolutionParameters--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]ImageOptionsandOperations--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.

   TransformationParameters--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]TransformationInitialization--align-bounding-boxes
            Initially align centers of bounding boxes of all images by translations [Thisisthedefault]--align-centers-of-mass
            Initially align centers of mass by translations

       --init-scales
            Initialize scale factors using first-order moments

   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]--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.

       groupwise_affine [options] image0 [image1 ...]