SYNOPSIS
mia-3dfuzzysegment -i <in-file> [options]DESCRIPTION
mia-3dfuzzysegment This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D imageOPTIONS
-
- -i --in-file=(input, required); io
- input image(s) to be segmenetd For supported file types see PLUGINS:3dimage/io
- -c --cls-file=(output); 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
- -o --b0-file=(output); io
- image corrected for intensity non-uniformity For supported file types see PLUGINS:3dimage/io
- -n --no-of-classes=3
- number of classesnumber of classes
- -r --residuum=0.1
- relative residuumrelative residuum
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
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: 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
- 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 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
AUTHOR(s)
Gert WollnyCOPYRIGHT
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'.