Provided by: cmtk_3.3.1-1.2build1_amd64 bug


       groupwise_warp - Nonrigid population registration


       groupwise_warp [options] affineGroupRegistration


       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').


   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>
            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]

   Multuresolution Parameters
       --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 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 ]

            Do not write average image.

            Use cubic interpolation for average image (default: linear)

   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>
            Set number of histogram bins for entropy evaluation.  [Default: disabled]

            Crop image histograms to make better use of histogram bins.

            Match all image histograms to template data (or first image, if no template image  is

            Frequetly  repeat  histogram-based  intensity matching to account for changing volume

       --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:

   Transformation Parameters
       --grid-spacing <double>
            Control point grid spacing.  [Default: 40]

            Use grid spacing that fits volume FOV

       --refine-grid <integer>, -r <integer>
            Number of times to refine transformation grid [default: 0].  [Default: 0]

   Transformation Constraint Options
       --zero-sum, -z
            Enforce zero-sum computation.

            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]

   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]

       --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 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 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.