Provided by: cmtk_2.1.0-1_amd64 bug

NAME

       warpx - B-spline nonrigid registration

SYNOPSIS

       warpx ReferenceImage FloatingImage InitialXform

DESCRIPTION

       This  program  performs nonrigid image registration using multi-resolution optimization of
       voxel-based image similarity  measures  and  a  multi-resolution  B-spline  transformation
       model.

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).

   Transformation import/export
       --initial <transformation-path>
            Initialize transformation from given path [Default: NONE]

       --invert-initial
            Invert given (affine) initial transformation.

       --write-itk-xform <transformation-path>
            Output path for final transformation in ITK format [Default: NONE]

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

   Transformation parameters
       --grid-spacing <double>
            Control point grid spacing [Default: 10]

       --grid-refine <integer>
            Number of refinements (control point grid resolution levels) [Default: 0]

       --delay-refine
            Delay control point grid refinement; first switch to next higher image resolution

       --exact-spacing
            Use  exact  control  point  spacing;  do  not  modify  spacing to fit reference image
            bounding box

       --ignore-edge <integer>
            Ignore n control point layers along each image face [Default: 0]

       --restrict <string>
            Restrict  deformation  to  coordinate  dimension(s)  [one  or  more  of  'x','y','z']
            [Default: NONE]

       --no-adaptive-fix
            Disable adaptive fixing of control points; optimize all deformation parameters

       --adaptive-fix-thresh <float>
            Threshold factor for entropy criterion to fix local control points [Default: 0.5]

       --accurate
            Accurate  computation  mode:  may  give  slightly  better results after substantially
            longer computation [This is the default]

       --fast
            Fast computation mode: may give slightly worse results than accurate mode, but  saves
            substantial CPU time

   Regularization parameters
       --jacobian-constraint-weight <float>
            Weight for Jacobian-based local volume preservation constraint [Default: 0]

       --smoothness-constraint-weight <float>
            Weight   for  smoothness  constraint  based  on  second-order  grid  bending  energy.
            [Default: 0]

       --landmark-constraint-weight <float>
            Weight for landmark misregistration registration [Default: 0]

       --inverse-consistency-weight <float>
            Weight for inverse consistency constraint [Default: 0]

       --constraint-relaxation-factor <float>
            Weight relaxation factor for alternating under-constrained iterations [Default: -1]

       --relax-to-unfold
            Before each resolution level, regularize negative-Jacobian areas of  the  deformation
            to unfold them.

   Optimization parameters
       --max-stepsize <double>
            Maximum  optimizer  step  size, which determines search space exploration.  [Default:
            -1]

       --min-stepsize <double>
            Minimum optimizer step size, which determines precision.  [Default: -1]

       --stepfactor <double>
            Factor for search step size reduction. Must  be  >  0.0  and  <  1.0  [default:  0.5]
            [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]

       --no-maxnorm
            Use Euclid norm for gradient normalication in optimization, rather than maximum norm

   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 for final registration stage.

   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.

       --repeat-match-histograms
            Repeat histogram matching after every level of the registration to account for volume
            changes. When registering masked data, it is  advisable  to  also  use  the  --force-
            outside-value option to prevent poorly matched histograms.

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

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

       --output-intermediate
            Write transformation for each level [default: only write final transformation]

   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).