Provided by: mia-tools_2.4.7-13_amd64 bug

NAME

       mia-3dfluid - Fluid dynamic 3D registration

SYNOPSIS

       mia-3dfluid -i <in-image> -r <ref-image> -o <out-transformation> [options]

DESCRIPTION

       mia-3dfluid  This  program  is  used for non-rigid registration based on fluid dynamics as
       described in:

              Wollny,  G.  and  Kruggel,  F.,  'Computational  cost  of  non-rigid   registration
              algorithms   based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8),
              pp. 946-952, 2002.  ⟨https://doi.org/10.1109/TMI.2002.803113⟩

        It uses SSD as the sole registration criterion.

OPTIONS

   File-IO
              -i --in-image=(input, required); io
                     input 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 --out-transformation=(output, required); io
                     output transformation comprising the registering transformation field
                      For supported file types see PLUGINS:3dtransform/io

              -d --out-image=(output); io
                     save deformed image
                      For supported file types see PLUGINS:3dimage/io

   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).

   Registration parameters
                 --disable-multigrid
                     disable multi-grid processing

                 --disable-fullres
                     disable processing on the full resolution image

                 --lambda=1
                     elasticy constant

                 --mu=1
                     elasticy constant

              -s --start-size=16
                     initial multigrided size

              -m --method=sora
                     method for solving PDE

                        sor ‐ successive overrelaxation
                        sora ‐ Gauss Southwell relexation

                 --step=0.8
                     Initial stepsize

              -p --interpolator=bspline:d=3
                     image interpolator kernel
                      For supported plugins see PLUGINS:1d/splinekernel

                 --relax=1
                     overrelaxation factor vor method sor

                 --maxiter=10
                     maximum iterations

                 --epsilon=0.01
                     truncation condition

                 --matter=4
                     intensity above which real matter is assumed (experimental)

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/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

EXAMPLE

       Register  image  test.v  to image ref.v and write the deformation vector field regfield.v.
       Start registration at the smallest size above 16 pixel.

       mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

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'.