bionic (1) mia-3dsegment-ahmed.1.gz
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 classes
-C --class-centres=
initial class centers, this parameter overrides 'no-of-clases'.
-s --spread=64
spread 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).
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. The orientation is transformed in the same way like it is done with
'dicomtonifti --no-reorder' from the vtk-dicom package.
('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
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'.