mia-3dcrispsegment(1)

📦
version 2.4.7 · 4 versions
, in ubuntu resolute, ubuntu stonking

💖 NAME 💖

mia-3dcrispsegment — label segmentation according to probabilities. Bestie, it's the glow-up from fuzzy to iconic labels. ✨

🦋 SYNOPSIS 🦋

mia-3dcrispsegment -i <in-file> -o <out-file> [options]

✨ DESCRIPTION ✨

So mia-3dcrispsegment takes a fuzzy segmentation and turns it into a label image, no cap. For each pixel, the label gets set to whichever class has the highest probability, plus a given offset that you get to pick. It's giving "argmax but make it fashion" 💅

🎀 OPTIONS 🎀

  • -i, --in-file=(input, required); io — the input class file. It should contain multiple images holding tissue class probabilities. For the supported file types, go peek at PLUGINS:3dimage/io 👀
  • -o, --out-file=(output, required); io — the output class label image. Again, supported file types live at PLUGINS:3dimage/io.
  • -l, --label-offset=1 — the label offset. Shift those labels, queen. Default is 1.

🫶 Help & Info

  • -V, --verbose=warning — how chatty the program is. It prints messages of the given level and higher priorities. 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 the copyright info 📜
  • -h, --help — print this help
  • -?, --usage — print a short help
  • --version — print the version number and exit

🔥 Processing

  • --threads=-1 — the max number of threads to use for processing (the manpage spells it "Maxiumum", and honestly? iconic). This number should be lower than or equal to the number of logical processor cores in your machine. -1 means automatic estimation, so it figures it out itself.

🌈 PLUGINS: 3dimage/io 🌈

Here's the whole roster of file formats this thing can vibe with. Every single one, fr fr, no skips.

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

🌸 EXAMPLE 🌸

Say you wanna set the labels based on the input class probability file cls.v, adding the offset 2 to each label, and save the result to labeled.v. Boom:

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

👑 AUTHOR(s) 👑

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.

Real talk bestie: that's the license, and the "no warranty" part is for real for real — no take-backs, no refunds, no drama 💀

That's the whole thing, start to finish. This page is from the USER COMMANDS crew, version v2.4.7, and it's the mia-3dcrispsegment(1) manual. Go label something, you absolute legend 🦋💖✨

📦 where this page comes from