.TH mia\-2dsegment\-ahmed 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-2dsegment\-ahmed
\- Run a fuzzy c\-means segmentation of a 2D image.
.SH SYNOPSIS
.B  mia\-2dsegment\-ahmed \-i <in\-file> \-o <out\-file> [options]
.SH DESCRIPTION
.B mia\-2dsegment\-ahmed
This program implements a variation of the paper:

.RS
.UR https://doi.org/10.1109/42.996338
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,
.UE
.RE

 changes are: p=2, and exp
.SH OPTIONS
.RS
.IP "\-i \-\-in-file=(input, required); io"
image to be segmented
 For supported file types see PLUGINS:2dimage/io
.IP "\-o \-\-out-file=(output, required); io"
class probability images, the image type must support multiple images and floating point values
 For supported file types see PLUGINS:2dimage/io
.IP "\-a \-\-no-of-classes=3"
number of classes

.IP "\-b \-\-bias-correct"
apply bias field correction

.IP "\-c \-\-class-centres="
initial class centers

.IP "\-s \-\-spread=64"
spread parameter describing the strength of mattar distinction

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