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

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

       registration - Rigid and affine 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.

       --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).

   AutomationOptions--auto-multi-levels<integer>
            Automatic optimization and resolution parameter generation for <n> levels [Default:0]Optimizationsettings--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]Imageresolutionparameters--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.

   Transformationparameters--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

   Imagedata--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 [Thisisthedefault]--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.

   ReferenceImagePreprocessing--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]FloatingImagePreprocessing--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]Outputparameters--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]ImportResultsintoSlicer--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/TransformationDatabase--db<string>
            Path  to  image/transformation  database  that  should  be  updated with the new registration and/or
            reformatted image.  [Default:NONE]

registration ReferenceImage FloatingImage