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'.