NAME

       mia-3dsegment-ahmed - Run a fuzzy c-means segmentation of a 3D image.

SYNOPSIS

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

DESCRIPTION

       mia-3dsegment-ahmed This program implements a variation of the paper:Mohamed N. Ahmed et. al, "A Modified
       Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans.  on  Medical
       Imaging, Vol. 21, No. 3, March 2002, changes are: p=2, and exp

OPTIONS

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

              -o --out-file=(required)
                     class  probability  images,  the image type must support multiple images and floating point
                     values  For supported file types see PLUGINS:3dimage/io

              -a --no-of-classes=3
                     number of classes

              -b --bias-correct
                     apply bias field correction

              -c --class-centres=
                     initial class centers

              -s --spread=64
                     spread parameter describing the strength of mattar distinction

   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

EXAMPLE

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

       mia-3dsegment-ahmed -i input.v -a 5 -o cls.v

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'.