NAME

       mia-2dfuzzysegment - A fuzzy c-means segmentation of a 2D image

SYNOPSIS

       mia-2dfuzzysegment -i <in-file> [options]

DESCRIPTION

       mia-2dfuzzysegment  This  program  runs  a  combined  fuzzy c-means clustering and B-field
       correction to facilitate a fuzzy segmentation of 2D image. cf D.L.  Pham  and  J.L.Prince,
       "An  adaptive  fuzzy C-means algorithm for image segmentation in the presence of intensity
       inhomogeneities", Pat. Rec. Let., 20:57-68,1999

OPTIONS

   File-IO
              -i --in-file=(input, required); io
                     input  image(s)  to   be   segmenetd    For   supported   file   types   see
                     PLUGINS:2dimage/io

              -c --cls-file=(output); io
                     output class probability images (floating point values and multi-image)  For
                     supported file types see PLUGINS:2dimage/io

              -o --b0-file=(output); io
                     image corrected for intensity non-uniformity  For supported file  types  see
                     PLUGINS:2dimage/io

              -g --gain-file=(output); io
                     gain   field   (floating   point  valued)   For  supported  file  types  see
                     PLUGINS:2dimage/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
              -n --no-of-classes=3
                     number of classesnumber of classes

              -r --residuum=0.1
                     relative residuumrelative residuum

                 --l1=200000
                     Penalize  magnitude  of intensity inhomogeinity correctionPenalize magnitude
                     of intensity inhomogeinity correction

                 --l2=2e+06
                     Smoothness of  intensity  inhomogeinity  correctionSmoothness  of  intensity
                     inhomogeinity correction

   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).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: 2dimage/io

       bmp       BMP 2D-image input/output support

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     2D image io for DICOM

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       signed 16 bit, unsigned 16 bit

       exr       a 2dimage io plugin for OpenEXR images

                     Recognized file extensions:  .EXR, .exr

                     Supported element types:
                       unsigned 32 bit, floating point 32 bit

       jpg       a 2dimage io plugin for jpeg gray scale images

                     Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg

                     Supported element types:
                       unsigned 8 bit

       png       a 2dimage io plugin for png images

                     Recognized file extensions:  .PNG, .png

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit

       raw       RAW 2D-image output support

                     Recognized file extensions:  .RAW, .raw

                     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

       tif       TIFF 2D-image input/output support

                     Recognized file extensions:  .TIF, .TIFF, .tif, .tiff

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

       vista     a 2dimage io plugin for vista images

                     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

EXAMPLE

       Run a 5-class segmentation over input image input.v and store the class probability images
       in cls.v and the B0-field corrected image in b0.v.

       mia-2dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

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'.