NAME

       mia-3dmaskseeded - Mask an area by seeded region growing

SYNOPSIS

       mia-3dmaskseeded -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-3dmaskseeded  3D  image  segmentation  based  on  region  growing  from  a seed point.
       Neighboring points are added, either when their intensity is equal or higher than that  of
       the  seed  point, or of the intensity is lower or equal then that of the neighoring point.
       After region growing is finished, this mask is used to zero out the region in the original
       image yielding the resulting image.

OPTIONS

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

              -o --out-file=(required)
                     output image(s) that have  been  filtered   For  supported  file  types  see
                     PLUGINS:3dimage/io

              -s --seed=[0,0,0]
                     seed point

              -n --neighborhood=6n
                     neighborhood shape  For supported plugins see PLUGINS:3dimage/shape

   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: 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/shape

       18n       18n neighborhood 3D shape creator

                     (no parameters)

       26n       26n neighborhood 3D shape creator

                     (no parameters)

       6n        6n neighborhood 3D shape creator

                     (no parameters)

       sphere    Closed  spherical  shape neighborhood including the pixels within a given radius
                 r., supported parameters are:

                     r = 2 (float)
                       sphere radius.  in [0, 3.40282e+38]

EXAMPLE

       Run  a  region  growing  on  input.v  starting  at  point  <10,23,21>  and  use  the   18n
       neighbourhood.

       mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

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'.