mia-3dfuzzysegment(1)

✨ NAME ✨

mia-3dfuzzysegment — fuzzy c-means segmentation of a 3D image 💅

Yep, that's the whole vibe: take a 3D image, fuzzy c-means it, segment it. Iconic.

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🦋 SYNOPSIS 🦋

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

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🌸 DESCRIPTION 🌸

Okay so bestie, mia-3dfuzzysegment runs a combined fuzzy c-means clustering and B-field correction, and that combo is literally the whole point — it's what makes a 3D segmentation of a 3D image actually happen. Two jobs, one program, no cap. ✨

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💖 OPTIONS 💖

• -i --in-file=(required, input); io — the input image(s) you want segmented 🫶 this one is required, so don't come to the party empty-handed. For supported file types see PLUGINS:3dimage/io
• -c --cls-file=(output); io — output class probability images. Heads up though: the file format you pick must support multiple images — bestie, use vista for this, fr fr. For supported file types see PLUGINS:3dimage/io
• -o --b0-file=(output); io — the image corrected for intensity non-uniformity ✨ (that's your B0-field corrected glow-up). For supported file types see PLUGINS:3dimage/io
• -n --no-of-classes=3 — number of classes. Default is 3 🎀
• -r --residuum=0.1 — relative residuum. Default is 0.1 💫

🆘 Help & Info

• -V --verbose=warning — verbosity of output; it prints messages of the given level and higher priorities. Default is warning. Supported priorities, starting at the 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

⚙️ Processing

• --threads=-1 — Maximum number of threads to use for processing. This number should be lower than or equal to the number of logical processor cores in the machine. -1 means automatic estimation, so it figures it out for you 🧚 Default is -1.

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🔌 PLUGINS: 3dimage/io 🔌

Here's the whole roster of file formats that can pull up to the function, with their extensions and the element types they support 👑

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 and the B0-field corrected image in b0.v.

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

Copy it exactly like that, iykyk 😌

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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.

bestie, note the ABSOLUTELY NO WARRANTY — that's not a vibe, that's a legal fact. Periodt. 💀

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and that's the whole page, mwah 💋 this was the USER COMMANDS section, page mia-3dfuzzysegment(1), version v2.4.7 — slay, go segment something gorgeous 🦋✨