NAME

       mia-2dsegment-ahmed - Run a fuzzy c-means segmentation of a 2D image.

SYNOPSIS

       mia-2dsegment-ahmed -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dsegment-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=(input, required); io
                     image to be segmented
                      For supported file types see PLUGINS:2dimage/io

              -o --out-file=(required, output); io
                     class  probability  images,  the image type must support multiple images and floating point
                     values
                      For supported file types see PLUGINS:2dimage/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:

                        trace ‐ Function call trace
                        debug ‐ Debug output
                        info ‐ Low level messages
                        message ‐ Normal messages
                        warning ‐ Warnings
                        fail ‐ Report test failures
                        error ‐ Report errors
                        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: 2dimage/io

       bmp       BMP 2D-image input/output support. The plug-in supports reading and writing  of  binary  images
                 and  8-bit  gray  scale  images. read-only support is provided for 4-bit gray scale images. The
                 color table is ignored and the pixel values are taken as literal gray scale values.

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 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.

       mia-2dsegment-ahmed -i input.v -a 5 -o 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'.