Provided by: mia-tools_2.4.7-8ubuntu1_amd64 bug

NAME

       mia-3dfluid-syn-registration   -   Non-linear   registration  of  3D  images  by  using  a
       diffeomorphic SyN registration

SYNOPSIS

       mia-3dfluid-syn-registration   -i   <in-image>   -r   <ref-image>   -o   <transform>    -O
       <inverse-transform> [options]

DESCRIPTION

       mia-3dfluid-syn-registration This program implements the registration of two gray scale 3D
       images. The transformation applied is a symmeric diffeomorpic fluid dynamic  registration.
       To  work most efficiently, this program makes a few assumptions about the imput data, i.e.
       the image must be of the same size, have the same voxel spacing, and any  intensity  range
       normalization or equalization should also be done before calling this program.

OPTIONS

   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

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

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

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

              -O --inverse-transform=(output, required); io
                     inverse output transformation
                      For supported file types see PLUGINS:3dtransform/io

   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).

   Registration
              -l --mg-levels=3
                     Number of multi-resolution levels to run the registration on. Not that  some
                     registration  parameters  can  be given as a coma seperated list to indicate
                     per level values. In these cases  if the number of given values  is  smaller
                     than  the  number  of multi-resolution levels (this parameter), the the last
                     given value is used for all subsequest multi-resolution levels.

              -S --step=0.25; float in (0, 0.5]
                     Initial step size for all levels

              -c --cost=ssd
                     Image similarity function to be minimized
                      For supported plugins see PLUGINS:3dimage/cost

              -R --regularizer=sor:kernel=fluid,maxiter=50
                     Regularization for the force to transformation update
                      For supported plugins see PLUGINS:3dvf/regularizer

              -T --conv-test-interval=; vuint in [4, 40]
                     Convergence test interations intervall: In order to measure convergence  the
                     cost  function  value  is  averaged  over this amount of iterations, and the
                     decline rate is evaluated  based  on  the  linare  regression  of  the  cost
                     function  values  in  this  intervall.  This  parameter  can  be  given as a
                     coma-seperated  list  with  values  corresponding  to  the  multi-resolution
                     levels, see option --mg-levels for more information.

              -D --stop-decline-rate=; vdouble in [0, inf)
                     Stopping  criterium  for registration based on the cost decline rate. If the
                     rate below this value, the iteration is stopped. This parameter can be given
                     as  a  coma-seperated list with values corresponding to the multi-resolution
                     levels, see option --mg-levels for more information.

              -C --stop-cost=
                     Stopping criterium for registration based on the cost  value.  If  the  cost
                     drops  below  this  value,  the  iteration is stopped. This parameter can be
                     given  as  a  coma-seperated  list  with   values   corresponding   to   the
                     multi-resolution levels, see option --mg-levels for more information.

              -I --iter=; vuint in [4, inf)
                     Naximum  number  if  iterations  done  on  each multi-resolution level. This
                     parameter can be given as a coma-seperated list with values corresponding to
                     the multi-resolution levels, see option --mg-levels for more information.

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: 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: 3dvf/regularizer

       sor       This plugin implements successive (over-)relaxation as a  solver  to  regularize
                 the vector field., supported parameters are:

                     abs_f = 0.01; float in [0, inf)
                       breaking condition: absolute residuum.

                     kernel = fluid; factory
                       solver    kernel    to    be    used.     For   supported   plug-ins   see
                       PLUGINS:3dvf/regularizerkernel

                     maxiter = 100; uint in [0, inf)
                       maximum number of iterations.

                     rel_f = 1e-05; float in (0, 1)
                       breaking condition: relative residuum.

PLUGINS: 3dvf/regularizerkernel

       fluid     Evaluation  kernel  for  the  fluid-dynamics  solver,  either  using  successive
                 (over-)relaxation,  or  a  Gauss-Southwell  relaxation.  This  implementation is
                 generic  and  doesn't  implement  any  architecture   specific   optimizations.,
                 supported parameters are:

                     lambda = 1; float in [0, 10000]
                       bulk viscosity (compressibility).

                     mu = 1; float in (0, 10000]
                       dynamic viscosity (shear).

                     relax = 1; float in [0.1, 2]
                       Relaxation parameter for the solver.

EXAMPLE

       Register  image  test.v  to  image  ref.v saving the transformation to transform.v and the
       inverse transform to inverse-transform.v. Use three multiresolution levels, ssd  as  image
       cost function.

       mia-3dfluid-syn-registration  -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l
              3 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'.