xenial (1) mia-3dsegment-ahmed.1.gz

Provided by: mia-tools_2.2.7-3_amd64 bug

NAME

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

SYNOPSIS

       mia-3dsegment-ahmed -i <in-file> -c <class-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

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

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

              -b --out-file=(output); io
                     Bias corrected image will be of the same type like the input image. If  this  parameter  is
                     not  given,  then  the  bias  correction will not be applied.  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
              -n --no-of-classes=3
                     number of classesnumber of classes

              -C --class-centres=
                     initial class centers, this parameter overrides 'no-of-clases'.

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

   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: 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

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

AUTHOR(s)

       Gert Wollny

       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'.