mia-3dsegment-ahmed(1)

🌸 mia-3dsegment-ahmed 🌸

okay bestie, pull up a chair, we're doing a fuzzy c-means segmentation of a 3D image and it's gonna be cute. this is part of the General Commands Manual family, so you already know it's a little command-line icon. 💅

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✨ NAME ✨

mia-3dsegment-ahmed — Run a fuzzy c-means segmentation of a 3D image.

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🦋 SYNOPSIS 🦋

mia-3dsegment-ahmed -i <in-file> -c <class-file> [options]

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💖 DESCRIPTION 💖

so mia-3dsegment-ahmed implements a variation of this paper, and I need you to respect it:

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,

and the changes are, no cap: p=2, and exp.

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🎀 OPTIONS 🎀

💾 File-IO

• -i, --in-file=(input, required); io — the image to be segmented, bestie. the main character, literally. For supported file types see PLUGINS:3dimage/io
• -c, --class-file=(output, required); io — class probability images. heads up: the image type must support multiple images and floating point values. yes that's a requirement, not a suggestion 🙈 For supported file types see PLUGINS:3dimage/io
• -b, --out-file=(output); io — the bias corrected image, and it'll be of the same type like the input image. if you don't pass this parameter, then the bias correction will not be applied. that's just how it is, fr fr. For supported file types see PLUGINS:3dimage/io

🫶 Help & Info

• -V, --verbose=warning — verbosity of output, prints messages of given level and higher priorities. supported priorities starting at lowest level are:
  • trace — Function call trace
  • debug — Debug output
  • info — Low level messages
  • message — Normal messages
  • warning — Warnings
  • fail — Report test failures
  • error — Report errors
  • 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' (yes, spelled exactly like that, we keep it real 💀).
• -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).

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🌈 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:

• 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

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🧚 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

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👑 AUTHOR(s) 👑

Gert Wollny

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💜 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'.

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okay that's the whole thing, you ate it. 🍓 now go segment something and be the main character of your own 3D image. ✨

USER COMMANDS · v2.4.7 · mia-3dsegment-ahmed(1) — mwah, logging off bestie 💅🦋