Provided by: mia-tools_2.0.13-1_amd64 bug

NAME

       mia-3dcost-translatedgrad  -  Evaluate the cost gradient between two images and convert it
       to a spline representation.

SYNOPSIS

       mia-3dcost-translatedgrad -i <in-file> -r <ref-file> -o <out-file> [options]

DESCRIPTION

       mia-3dcost-translatedgrad Evaluate the cost gradient between two images and  evaluate  the
       transformation related gradient for it based on the given transformation model.

OPTIONS

              -i --in-file=(required)
                     input image   For supported file types see PLUGINS:3dimage/io

              -r --ref-file=(required)
                     reference image   For supported file types see PLUGINS:3dimage/io

              -o --out-file=(required)
                     output vector field   For supported file types see PLUGINS:3dtransform/io

              -g --gradimg-file=
                     norm  image of the spline transformed gradient  For supported file types see
                     PLUGINS:3dimage/io

              -C --cost-gradimg-file=
                     norm  image  of  the  cost  gradient    For   supported   file   types   see
                     PLUGINS:3dimage/io

              -f --transForm=spline:rate=5
                     Transformation   the   gradient   relates  to   For  supported  plugins  see
                     PLUGINS:3dimage/transform

              -c --cost=ssd
                     cost function to use  For supported plugins see PLUGINS:3dimage/cost

   Help & Info
              -V --verbose=warning
                     verbosity of output, print messages of given level  and  higher  priorities.
                     Supported priorities starting at lowest level are:
                        info ‐ Low level messages
                        warning ‐ Warnings
                        error ‐ Report errors
                        fail ‐ Report test failures
                        message ‐ Normal messages
                        fatal ‐ Report only fatal errors

                 --copyright
                     print copyright information

              -h --help
                     print this help

              -? --usage
                     print a short help

                 --version
                     print the version number and exit

   Processing
                 --threads=-1
                     Maxiumum number of threads to use for processing,This number should be lower
                     or equal to the number of logical  processor  cores  in  the  machine.  (-1:
                     automatic estimation).

PLUGINS: 1d/splinebc

       mirror    Spline interpolation boundary conditions that mirror on the boundary

                     (no parameters)

       repeat    Spline interpolation boundary conditions that repeats the value at the boundary

                     (no parameters)

       zero      Spline interpolation boundary conditions that assumes zero for values outside

                     (no parameters)

PLUGINS: 1d/splinekernel

       bspline   B-spline kernel creation , supported parameters are:

                     d = 3 (int)
                       Spline degree.  in [0, 5]

       omoms     OMoms-spline kernel creation, supported parameters are:

                     d = 3 (int)
                       Spline degree.  in [3, 3]

PLUGINS: 3dimage/cost

       mi        Spline parzen based mutual information., supported parameters are:

                     cut = 0 (float)
                       Percentage  of  pixels  to  cut  at  high  and  low  intensities to remove
                       outliers.  in [0, 40]

                     mbins = 64 (uint)
                       Number of histogram bins used for the moving image.  in [1, 256]

                     mkernel = [bspline:d=3] (factory)
                       Spline kernel for moving image parzen hinstogram.  For supported  plug-ins
                       see PLUGINS:1d/splinekernel

                     rbins = 64 (uint)
                       Number of histogram bins used for the reference image.  in [1, 256]

                     rkernel = [bspline:d=0] (factory)
                       Spline  kernel for reference image parzen hinstogram.  For supported plug-
                       ins see PLUGINS:1d/splinekernel

       ngf       This function evaluates  the  image  similarity  based  on  normalized  gradient
                 fields. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the
                 ref image various evaluators are implemented., supported parameters are:

                     eval = ds (string)
                       plugin subtype (sq, ds,dot,cross).

       ssd       3D image cost: sum of squared differences, supported parameters are:

                     norm = 0 (bool)
                       Set whether the metric should be normalized by the number of image pixels.

PLUGINS: 3dimage/io

       analyze   Analyze 7.5 image

                     Recognized file extensions:  .HDR, .hdr

                     Supported element types:
                       unsigned 8 bit, signed 16 bit, signed  32  bit,  floating  point  32  bit,
                       floating point 64 bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     Dicom image series as 3D

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       unsigned 16 bit

       inria     INRIA image

                     Recognized file extensions:  .INR, .inr

                     Supported element types:
                       signed  8  bit,  unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
                       bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

       mhd       MetaIO 3D image IO using the VTK implementation (experimental).

                     Recognized file extensions:  .MHA, .MHD, .mha, .mhd

                     Supported element types:
                       signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16  bit,  signed  32
                       bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

       vff       VFF Sun raster format

                     Recognized file extensions:  .VFF, .vff

                     Supported element types:
                       unsigned 8 bit, signed 16 bit

       vista     Vista 3D

                     Recognized file extensions:  .V, .VISTA, .v, .vista

                     Supported element types:
                       binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit,
                       signed 32 bit, unsigned 32 bit, floating point 32 bit, floating  point  64
                       bit

       vti       3D image VTK-XML in- and output (experimental).

                     Recognized file extensions:  .VTI, .vti

                     Supported element types:
                       signed  8  bit,  unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
                       bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

       vtk       3D VTK image legacy in- and output (experimental).

                     Recognized file extensions:  .VTK, .VTKIMAGE, .vtk, .vtkimage

                     Supported element types:
                       signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16  bit,  signed  32
                       bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

PLUGINS: 3dimage/transform

       affine    Affine transformation (12 degrees of freedom), supported parameters are:

                     imgboundary = mirror (factory)
                       image  interpolation  boundary  conditions.   For  supported  plug-ins see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image    interpolator    kernel.     For    supported     plug-ins     see
                       PLUGINS:1d/splinekernel

       rigid     Rigid  transformation,  i.e. rotation and translation (six degrees of freedom).,
                 supported parameters are:

                     imgboundary = mirror (factory)
                       image interpolation  boundary  conditions.   For  supported  plug-ins  see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image     interpolator     kernel.     For    supported    plug-ins    see
                       PLUGINS:1d/splinekernel

                     rot-center = [[0,0,0]] (streamable)
                       Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of
                       the volume.

       rotation  Rotation transformation (three degrees of freedom)., supported parameters are:

                     imgboundary = mirror (factory)
                       image  interpolation  boundary  conditions.   For  supported  plug-ins see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image    interpolator    kernel.     For    supported     plug-ins     see
                       PLUGINS:1d/splinekernel

                     rot-center = [[0,0,0]] (streamable)
                       Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of
                       the volume.

       spline    Free-form transformation that can be described by a set of B-spline coefficients
                 and an underlying B-spline kernel., supported parameters are:

                     anisorate = [[0,0,0]] (3dfvector)
                       anisotropic  coefficient  rate  in  pixels,  nonpositive  values  will  be
                       overwritten by the 'rate' value..

                     debug = 0 (bool)
                       enable additional debuging output.

                     imgboundary = mirror (factory)
                       image interpolation  boundary  conditions.   For  supported  plug-ins  see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image     interpolator     kernel.     For    supported    plug-ins    see
                       PLUGINS:1d/splinekernel

                     kernel = [bspline:d=3] (factory)
                       transformation   spline    kernel.     For    supported    plug-ins    see
                       PLUGINS:1d/splinekernel

                     penalty =  (factory)
                       transformation   penalty   energy   term.    For  supported  plug-ins  see
                       PLUGINS:3dtransform/splinepenalty

                     rate = 10 (float)
                       isotropic coefficient rate in pixels.  in [1, 3.40282e+38]

       translate Translation (three degrees of freedom), supported parameters are:

                     imgboundary = mirror (factory)
                       image interpolation  boundary  conditions.   For  supported  plug-ins  see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image     interpolator     kernel.     For    supported    plug-ins    see
                       PLUGINS:1d/splinekernel

       vf        This plug-in implements a transformation that defines  a  translation  for  each
                 point  of  the  grid  defining  the  domain  of  the  transformation., supported
                 parameters are:

                     imgboundary = mirror (factory)
                       image interpolation  boundary  conditions.   For  supported  plug-ins  see
                       PLUGINS:1d/splinebc

                     imgkernel = [bspline:d=3] (factory)
                       image     interpolator     kernel.     For    supported    plug-ins    see
                       PLUGINS:1d/splinekernel

PLUGINS: 3dtransform/io

       bbs       Binary (non-portable) serialized IO of 3D transformations

                     Recognized file extensions:  .bbs

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       vista     Vista storage of 3D transformations

                     Recognized file extensions:  .v, .v3dt

       xml       XML serialized IO of 3D transformations

                     Recognized file extensions:  .x3dt

PLUGINS: 3dtransform/splinepenalty

       divcurl   divcurl penalty on the transformation, supported parameters are:

                     curl = 1 (float)
                       penalty weight on curl.  in [0, 3.40282e+38]

                     div = 1 (float)
                       penalty weight on divergence.  in [0, 3.40282e+38]

                     weight = 1 (float)
                       weight of penalty energy.  in [0, 3.40282e+38]

EXAMPLE

       Evaluate  the  SSD  cost  between  src.v  and  ref.v  and  store  the  gradient   gradient
       corresponding to a spline transformation in grad.v3dt.

       mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd

AUTHOR(s)

       Gert Wollny

COPYRIGHT

       This  software  is  Copyright  (c) 1999‐2013 Leipzig, Germany and Madrid, Spain.  It comes
       with  ABSOLUTELY  NO WARRANTY  and  you  may redistribute it under the terms  of  the  GNU
       GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the
       option '--copyright'.