Provided by: mia-tools_2.4.7-13_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); io
                     input image
                      For supported file types see PLUGINS:3dimage/io

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

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

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

              -C --cost-gradimg-file=(output); io
                     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:

                        trace ‐ Function call trace
                        debug ‐ Debug output
                        info ‐ Low level messages
                        message ‐ Normal messages
                        warning ‐ Warnings
                        fail ‐ Report test failures
                        error ‐ Report errors
                        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 in [0, 5]
                       Spline degree.

       omoms     OMoms-spline kernel creation, supported parameters are:

                     d = 3; int in [3, 3]
                       Spline degree.

PLUGINS: 3dimage/cost

       lncc      local normalized cross correlation with masking support.,  supported  parameters
                 are:

                     w = 5; uint in [1, 256]
                       half  width  of  the  window  used  for  evaluating  the  localized  cross
                       correlation.

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

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

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

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

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

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

       ncc       normalized cross correlation.

                     (no parameters)

       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; dict
                       plugin subtype (sq, ds,dot,cross).  Supported values are:
                           ds ‐ square of scaled difference
                           dot ‐ scalar product kernel
                           cross ‐ cross product kernel

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

                     autothresh = 0; float in [0, 1000]
                       Use automatic masking of the moving image by only takeing intensity values
                       into accound that are larger than the given threshold.

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

       ssd-automask
                 3D image cost: sum of squared  differences,  with  automasking  based  on  given
                 thresholds, supported parameters are:

                     rthresh = 0; double
                       Threshold intensity value for reference image.

                     sthresh = 0; double
                       Threshold intensity value for source image.

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:
                       signed 16 bit, unsigned 16 bit

       hdf5      HDF5 3D image IO

                     Recognized file extensions:  .H5, .h5

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

       nifti     NIFTI-1 3D image IO. The orientation is transformed in the same way like  it  is
                 done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

                     Recognized file extensions:  .NII, .nii

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

       axisrot   Restricted rotation transformation (1 degrees of freedom). The transformation is
                 restricted to the rotation around  the  given  axis  about  the  given  rotation
                 center, supported parameters are:

                     axis =(required, 3dfvector)
                       rotation axis.

                     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

                     origin =(required, 3dfvector)
                       center of the transformation.

       raffine   Restricted  affine  transformation (3 degrees of freedom). The transformation is
                 restricted to the rotation around the given axis and shearing along the two axis
                 perpendicular to the given one, supported parameters are:

                     axis =(required, 3dfvector)
                       rotation axis.

                     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

                     origin =(required, 3dfvector)
                       center of the transformation.

       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

                     origin = [[0,0,0]]; 3dfvector
                       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

                     origin = [[0,0,0]]; 3dfvector
                       Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of
                       the volume.

       rotbend   Restricted  transformation  (4  degrees  of  freedom).  The  transformation   is
                 restricted  to  the  rotation  around the x and y axis and a bending along the x
                 axis, independedn in each  direction,  with  the  bending  increasing  with  the
                 squared distance from the rotation axis., 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

                     norot = 0; bool
                       Don't optimize the rotation.

                     origin =(required, 3dfvector)
                       center of the transformation.

       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 debugging 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 in [1, inf)
                       isotropic coefficient rate in pixels.

       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 in [0, inf)
                       penalty weight on curl.

                     div = 1; float in [0, inf)
                       penalty weight on divergence.

                     norm = 0; bool
                       Set  to  1  if  the penalty should be normalized with respect to the image
                       size.

                     weight = 1; float in (0, inf)
                       weight of penalty energy.

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) 1999‐2015 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'.