Provided by: cmtk_2.1.0-1_amd64 bug

NAME

       registration - Rigid and affine registration

SYNOPSIS

       registration ReferenceImage FloatingImage

DESCRIPTION

       This   program  performs  rigid  and  affine  image  registration  using  multi-resolution
       optimization of voxel-based image similarity measures.

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.

       --xml
            Write command line syntax specification in XML markup (for Slicer integration).

       --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).

   Automation Options
       --auto-multi-levels <integer>
            Automatic optimization and resolution parameter generation for <n>  levels  [Default:
            0]

   Optimization settings
       --exploration <double>, -e <double>
            Exploration [initial optimizer step size] [Default: 8]

       --accuracy <double>, -a <double>
            Accuracy [final optimizer step size] [Default: 0.1]

       --stepfactor <double>, -f <double>
            Factor for search step size reduction. Must be > 0.0 and < 1.0 [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]

   Image resolution parameters
       --sampling <double>, -s <double>
            Image sampling (finest resampled image resolution) [Default: 1]

       --coarsest <double>
            Upper limit for image sampling in multiresolution hierarchy [Default: -1]

       --omit-original-data
            Do not use original data in full resolution,  omit  final  stage  in  multiresolution
            hierarchy, thus reducing computation time.

   Transformation parameters
       --dofs <integer>[,<integer>,...]
            Add number of degrees of freedom [can be repeated]

       --dofs-final <integer>[,<integer>,...]
            Add number of degrees of freedom for final level only [can be repeated]

       --no-switch, -n
            Do   not   auto-switch  reference  and  floating  image  for  improved  computational
            performance

       --initxlate, -i
            Initialized transformation by translating floating image FOV  center  onto  reference
            image FOV center

       --initial <transformation-path>
            Initialize transformation from given path [Default: NONE]

       --initial-is-inverse
            Invert initial transformation before initializing registration

   Image data
       --registration-metric
            Registration  metric for motion estimation by image-to-image registration.  Supported
            values: "nmi", "mi", "cr", "msd", "ncc", where the default is "nmi", or  use  one  of
            the following:

            --nmi
                 Normalized Mutual Information metric [This is the default]

            --mi Standard Mutual Information metric

            --cr Correlation Ratio metric

            --msd
                 Mean Squared Difference metric

            --ncc
                 Normalized Cross Correlation metric

       --match-histograms
            Match floating image histogram to reference image histogram.

   Reference Image Preprocessing
       --class-ref <string>
            Data class: grey (default) or label [Default: NONE]

       --pad-ref <double>
            Padding value [Default: disabled]

       --thresh-min-ref <double>
            Minimum value truncation threshold [Default: disabled]

       --thresh-max-ref <double>
            Maximum value truncation threshold [Default: disabled]

       --prune-histogram-ref <integer>
            Number of bins for histogram-based pruning [Default: disabled]

       --histogram-equalization-ref
            Apply histogram equalization

       --sobel-filter-ref
            Apply Sobel edge detection filter

       --crop-index-ref <string>
            Cropping   region  in  pixel  index  coordinates  [parsed  as  %d,%d,%d,%d,%d,%d  for
            i0,j0,k0,i1,j1,k1] [Default: NONE]

       --crop-world-ref <string>
            Cropping   region   in   world   coordinates   [parsed   as   %f,%f,%f,%f,%f,%f   for
            x0,y0,z0,x1,y1,z1] [Default: NONE]

   Floating Image Preprocessing
       --class-flt <string>
            Data class: grey (default) or label [Default: NONE]

       --pad-flt <double>
            Padding value [Default: disabled]

       --thresh-min-flt <double>
            Minimum value truncation threshold [Default: disabled]

       --thresh-max-flt <double>
            Maximum value truncation threshold [Default: disabled]

       --prune-histogram-flt <integer>
            Number of bins for histogram-based pruning [Default: disabled]

       --histogram-equalization-flt
            Apply histogram equalization

       --sobel-filter-flt
            Apply Sobel edge detection filter

       --crop-index-flt <string>
            Cropping   region  in  pixel  index  coordinates  [parsed  as  %d,%d,%d,%d,%d,%d  for
            i0,j0,k0,i1,j1,k1] [Default: NONE]

       --crop-world-flt <string>
            Cropping   region   in   world   coordinates   [parsed   as   %f,%f,%f,%f,%f,%f   for
            x0,y0,z0,x1,y1,z1] [Default: NONE]

   Output parameters
       --outlist <string>, -o <string>
            Output path for final transformation [Default: NONE]

       --out-matrix <string>
            Output path for final transformation in matrix format [Default: NONE]

       --out-parameters <string>
            Output path for final transformation in plain parameter list format [Default: NONE]

       --protocol <string>, -p <string>
            Optimization protocol output file name [Default: NONE]

       --time <string>, -t <string>
            Computation time statistics output file name [Default: NONE]

   Import Results into Slicer
       --out-itk <transformation-path>
            Output path for final transformation in ITK format [Default: NONE]

       --write-reformatted <image-path>
            Write reformatted floating image.  [Default: NONE]

   Image/Transformation Database
       --db <string>
            Path   to   image/transformation  database  that  should  be  updated  with  the  new
            registration and/or reformatted image.  [Default: NONE]

AUTHORS

       Torsten Rohlfing, Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported  by
       the  National  Institute  of  Biomedical  Imaging  and  Bioengineering  under Grant No.R01
       EB008381 (PI: Torsten Rohlfing).