Provided by: cmtk_3.3.1p2+dfsg-1build1_amd64 bug

NAME

       registrationx - Rigid and affine registration

SYNOPSIS

       registrationx 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
       --max-stepsize <double>
            Maximum optimizer step size, which determines search space exploration.  [Default: 8]

       --min-stepsize <double>
            Minimum optimizer step size, which determines precision.  [Default: 0.1]

       --stepfactor <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. This can be 3 (translation), 6 (rigid: translation
            and rotation), 7 (rigid plus global scale), 9 (rigid  plus  anisotropic  scales),  12
            (rigid  plus  scales  plus shears), 3003 (translation plus shear), 3033 (translation,
            shear, and scale) or 3303 (rigid plus shears, but  no  scale).  This  option  can  be
            repeated,  in  which case DOFs are used for successive optimization runs in the order
            that they appear.

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

       --symmetric
            Use symmetric registration functional to simultaneously estimate forward and  inverse
            transformation.  This increases ragistration time substantially but produces a result
            that is invariant under exchange of fixed and moving  image.  It  may  also  be  more
            robust and/or more accurate than forward-only registration.

       --restrict-in-plane
            Restrict the affine transformation to be in-plane for planes perpendicular to a given
            coordinate axis.  Supported values: "xy", "xz", "yz", "none", where  the  default  is
            "none", or use one of the following:

            --xy Transformation  restricted  to  in-plane  for  'xy'  plane  (perpendicular  to z
                 coordinate axis).

            --xz Transformation restricted  to  in-plane  for  'xz'  plane  (perpendicular  to  y
                 coordinate axis).

            --yz Transformation  restricted  to  in-plane  for  'yz'  plane  (perpendicular  to x
                 coordinate axis).

            --none
                 Full 3D affine transformation is computed.  [This is the default]

       --init
            Select initializer for the affine trasnformation.  Supported values:  "none",  "fov",
            "com", "pax", "physical", where the default is "fov", or use one of the following:

            --none
                 Use input transformation, or identity transformation if none was provided.

            --fov
                 Align  centers of field of view (or crop regions) using a translation.  [This is
                 the default]

            --com
                 Align centers of mass using a translation.

            --pax
                 Align images by rotation using principal axes and translation using  centers  of
                 mass.

            --physical
                 Align  images  by  rotation  using  direction vectors stored in input images and
                 translation using image origins.

       --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", "rms", "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

            --rms
                 Root of Mean Squaresa metric (this is the square root of MSD)

            --msd
                 Mean Squared Difference metric

            --ncc
                 Normalized Cross Correlation metric

   Floating Image Interpolation Options
       --interpolation
            Interpolation  method  for  floating  image  sampling:  Supported  values:  "nearest-
            neighbor", "linear", "cubic", "cosine-sinc", "partial-volume", "automatic", where the
            default is "automatic", or use one of the following:

            --nearest-neighbor
                 Nearest neighbor interpolation (for intensity and label data)

            --linear
                 Trilinear interpolation

            --cubic
                 Tricubic interpolation

            --cosine-sinc
                 Cosine-windowed sinc interpolation (most accurate but slowest)

            --partial-volume
                 Partial volume interpolation (for label data)

            --automatic
                 Select interpolation automatically based on data  type:  linear  for  grey-level
                 data, nearest neighbor for label data.  [This is the default]

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

       --force-outside-value <double>
            Force  values  outside  field of view to this value rather than drop incomplete pixel
            pairs [Default: disabled]

   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

       --median-filter-radius-ref <integer>
            Apply median filter with given radius [Default: 0]

       --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]

       --crop-thresh-ref <double>
            Automatic cropping based on threshold [Default: disabled]

   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

       --median-filter-radius-flt <integer>
            Apply median filter with given radius [Default: 0]

       --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]

       --crop-thresh-flt <double>
            Automatic cropping based on threshold [Default: disabled]

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

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

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

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

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

   Import Results into Slicer
       --write-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,  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.