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

NAME

       ('mia\-3dsegment\-local\-cmeans',) - Run a c-means segmentation of a 3D image.

SYNOPSIS

       mia-3dsegment-local-cmeans -i <in-file> [options]

DESCRIPTION

       mia-3dsegment-local-cmeans  This program runs the segmentation of a 3D image by applying a
       localized c-means approach that helps to overcome intensity inhomogeneities in the  image.
       The  approach  evaluates  a  global  c-means clustering, and then separates the image into
       overlapping regions where more c-means iterations  are  run  only  including  the  locally
       present  classes,  i.e.  the  classes  that  relatively  contain  more pixels than a given
       threshold.

OPTIONS

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

              -o --out-file=(output); io
                     class label image based on merging local labels
                      For supported file types see PLUGINS:3dimage/io

              -G --out-global-crisp=(output); io
                     class label image based on global segmentation
                      For supported file types see PLUGINS:3dimage/io

              -C --class-prob=(output); io
                     class  probability  image  file,  filetype  must  support   floating   point
                     multi-frame images
                      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:

                        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

   Parameters
              -g --grid-spacing=15; int in [3, inf)
                     Spacing of the grid used to modulate the intensity inhomogeneities

              -c --cmeans=kmeans:nc=3
                     c-means initializer
                      For supported plugins see PLUGINS:1d/cmeans

              -e --c-means-epsilon=0.0001; float in (0, inf)
                     c-means breaking condition for update tolerance

              -t --relative-cluster-threshold=0.02; double in [0, 1)
                     threshhold to ignore classes when initializing the  local  cmeans  from  the
                     global one.

              -B --ignore-background
                     Don't  take  background  probablities  into  account  when  desiding whether
                     classes are to be ignored

              -L --label-threshold=0; float in [0, 1]
                     for values <= 0.5: create segmentation based on highest  class  probability,
                     labels  start  at  0.  For values >0.5: create labels only for voxels with a
                     class probability higher than the given value, labels start at 1 and  voxels
                     without an according class probability are set to 0; this output is suitable
                     for the seeded watershed filter.

   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/cmeans

       even      C-Means initializer that sets the initial class centers  as  evenly  distributed
                 over [0,1], supported parameters are:

                     nc =(required, ulong)
                       Number of classes to use for the fuzzy-cmeans classification.

       kmeans    C-Means  initializer  that  sets  the  initial  class centers by using a k-means
                 classification, supported parameters are:

                     nc =(required, ulong)
                       Number of classes to use for the fuzzy-cmeans classification.

       predefined
                 C-Means initializer that sets pre-defined values for the initial class  centers,
                 supported parameters are:

                     cc =(required, vdouble)
                       Initial  class  centers  fuzzy-cmeans  classification (normalized to range
                       [0,1]).

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

EXAMPLE

       Run the segmentation on image test.png using three classes, local  regions  of  40  pixels
       (grid width 20 pixels), and a class ignore threshold of 0.01.

       mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

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'.