Provided by: mia-tools_2.4.6-4ubuntu2_amd64 bug

NAME

       ('mia\-3disosurface\-from\-volume',) - Extract an ist-surface froma a 3D image.

SYNOPSIS

       mia-3disosurface-from-volume -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-3disosurface-from-volume This program is used to extract an iso-surface from the input
       gray scale image by using marching thetrahedra.

OPTIONS

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

              -o --out-file=(output, required); io
                     output mesh
                      For supported file types see PLUGINS:mesh/io

   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
                        trace ‐ Function call trace
                        fail ‐ Report test failures
                        warning ‐ Warnings
                        error ‐ Report errors
                        debug ‐ Debug output
                        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

   Image options
              -s --iso-value=128
                     iso-value of iso surface to be extracted

              -b --bordered
                     put an empty border around the image to ensure a closed surface

   Mesh options
              -f --max-faces=-1
                     maximum number of Faces,

              -e --max-edges=-1
                     maximum number of Edges

              -c --max-cost=0.1
                     maximum cost for edge collaps

              -r --ratio=4
                     ratio  of  faces(edges) to target number, at which  the optimization changes
                     from edge-length to volume-optimized

              -w --reverse-winding
                     reverse the winding of the triangles in order to  make  normals  point  away
                     from the high intensity area

   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: 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: mesh/io

       datapool  Virtual IO to and from the internal data pool

                     ('Recognized file extensions: ', '.@')

       off       plugin to load/store some Geomview OFF files. Supported is only the ASCII format
                 3D meshes with normales and per-vertex RGB  colors.  Alpha  values  and  texture
                 coordinates,  as  well as per face properties are ignored. Polygons are read and
                 triangulated.

                     ('Recognized file extensions: ', '.OFF, .off')

       ply       Ply triangle mesh input/output support

                     ('Recognized file extensions: ', '.PLY, .ply')

       stl       STL mesh io plugin

                     ('Recognized file extensions: ', '.STL, .stl')

       vista     Vista/Simbio triangle mesh input/output support

                     ('Recognized file extensions: ', '.-, .V, .VMESH, .v, .vmesh')

       vtk       A subset of VTK mesh in-and output: Triangle meshes are  written,  and  triangle
                 meshes  and  triangle  strips  are  read.  Additional  per-vertex attributes are
                 supported: 'normals', 'colors' for three component colors,  and  'scale'  for  a
                 scalar   value   attached   to   each   vertex.  The  data  is  written  by  the
                 vtkPolyDataWriter in binary format.

                     ('Recognized file extensions: ', '.VTK, .VTKMESH, .vtk, .vtkmesh')

EXAMPLE

       Extract the surface corresponding to the value  30  and  stop  optimizing  when  the  mesh
       consists of less than 100000 triangles.

       mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

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'.