DOKK / manpages / debian 10 / mia-tools / mia-3dfuzzysegment.1.en
mia-3dfuzzysegment(1) General Commands Manual mia-3dfuzzysegment(1)

('mia\-3dfuzzysegment',) - Fuzzy c-means segmentation of a 3D image.

mia-3dfuzzysegment -i <in-file> [options]

mia-3dfuzzysegment This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image

input image(s) to be segmenetd
For supported file types see PLUGINS:3dimage/io
output class probability images. Note, the used file format must support multible images (best is to use vista)
For supported file types see PLUGINS:3dimage/io
image corrected for intensity non-uniformity
For supported file types see PLUGINS:3dimage/io
number of classes

relative residuum

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
print copyright information

print this help

-? --usage
print a short help

print the version number and exit

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).

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

Virtual IO to and from the internal data pool

('Recognized file extensions: ', '.@')

Dicom image series as 3D

('Recognized file extensions: ', '.DCM, .dcm')

Supported element types:
signed 16 bit, unsigned 16 bit

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 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

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-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 Sun raster format

('Recognized file extensions: ', '.VFF, .vff')

Supported element types:
unsigned 8 bit, signed 16 bit

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

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

3D VTK image legacy in- and output (experimental).

('Recognized file extensions: ', '.VTK, .VTKIMAGE, .vtk, .vtkimage')

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

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-3dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

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'.

v2.4.6 USER COMMANDS