NAME

       groupwise_warp - Nonrigid population registration

SYNOPSIS

       groupwise_warp [options] affineGroupRegistration

DESCRIPTION

       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').

OPTIONS

   Global Toolkit Options (these are shared by all CMTK tools)
       --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).

   Registration Metric Options
       --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 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 ]

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

       --average-cubic
            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-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]

   Transformation Parameters
       --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]

   Transformation Constraint Options
       --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]

   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-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.

AUTHORS

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

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       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.