.TH mia\-2dfuzzysegment 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-2dfuzzysegment
\- A fuzzy c\-means segmentation of a 2D image
.SH SYNOPSIS
.B  mia\-2dfuzzysegment \-i <in\-file> [options]
.SH DESCRIPTION
.B 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
.SH OPTIONS
.SS File-IO
.RS
.IP "\-i \-\-in-file=(input, required); io"
input image(s) to be segmenetd
 For supported file types see PLUGINS:2dimage/io
.IP "\-c \-\-cls-file=(output); io"
output class probability images (floating point values and multi\-image)
 For supported file types see PLUGINS:2dimage/io
.IP "\-o \-\-b0-file=(output); io"
image corrected for intensity non\-uniformity
 For supported file types see PLUGINS:2dimage/io
.IP "\-g \-\-gain-file=(output); io"
gain field (floating point valued)
 For supported file types see PLUGINS:2dimage/io
.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Parameters
.RS
.IP "\-n \-\-no-of-classes=3"
number of classes

.IP "\-r \-\-residuum=0.1"
relative residuum

.IP "   \-\-l1=200000"
Penalize magnitude of intensity inhomogeinity correction

.IP "   \-\-l2=2e+06"
Smoothness of intensity inhomogeinity correction

.RE
.SS Processing
.RS
.IP "   \-\-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).

.RE
.SH PLUGINS: 2dimage/io
.TP 10
.B 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.
.P
.RS 14
Recognized file extensions:  .BMP, .bmp
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit
.RE
 
.RE
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
Recognized file extensions:  .@
.RE
 
.TP 10
.B dicom
2D image io for DICOM
.P
.RS 14
Recognized file extensions:  .DCM, .dcm
.RE
 
.RS 14
Supported element types: 
.RS 2
signed 16 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B exr
a 2dimage io plugin for OpenEXR images
.P
.RS 14
Recognized file extensions:  .EXR, .exr
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 32 bit, floating point 32 bit
.RE
 
.RE
.TP 10
.B jpg
a 2dimage io plugin for jpeg gray scale images
.P
.RS 14
Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit
.RE
 
.RE
.TP 10
.B png
a 2dimage io plugin for png images
.P
.RS 14
Recognized file extensions:  .PNG, .png
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B raw
RAW 2D-image output support
.P
.RS 14
Recognized file extensions:  .RAW, .raw
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B tif
TIFF 2D-image input/output support
.P
.RS 14
Recognized file extensions:  .TIF, .TIFF, .tif, .tiff
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
.RE
 
.RE
.TP 10
.B vista
a 2dimage io plugin for vista images
.P
.RS 14
Recognized file extensions:  .-, .V, .VISTA, .v, .vista
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.SH 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.
.HP
mia\-2dfuzzysegment \-i input.v \-c 5 \-o b0.v \-c cls.v
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.