Provided by: cmtk_3.0.0-1ubuntu1_amd64 bug


       groupwise_affine - Affine population registration


       groupwise_affine [options] image0 [image1 ...]


       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').


   Global Toolkit Options (these are shared by all CMTK tools)
            Write list of basic command line options to standard output.

            Write complete list of basic and advanced command line options to standard output.

            Write list of command line options to standard output in MediaWiki markup.

            Write man page source in 'nroff' markup to standard output.

            Write toolkit version to standard output.

            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).

   Registration Metric Options
            Use the RMI (a.k.a. regional mutual information) metric to drive the registration).

            Use   the   congealing  algorithm  using  pixelwise  stack  entropies  to  drive  the
            registration.  [This is the default]

   Template Image Options
       --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 Options
       --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 ]

            Use linear interpolation for average image [This is the default]

            Use cubic interpolation for average image

            Do not write average image.

   Multiresolution Parameters
       --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]

   Image Options and Operations
       --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 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  all image histograms to template data (or first image, if no template image is

            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.

   Transformation Parameters
       --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]

   Transformation Initialization
            Initially  align centers of bounding boxes of all images by translations [This is the

            Initially align centers of mass by translations

            Initialize scale factors using first-order moments

   Optimization Parameters
       --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 and output initial configuration.


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



       Report bugs at


       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.