mia-3dmaskseeded(1)

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

💖 mia-3dmaskseeded(1) — the glow-up guide 💖

okay bestie, so this is the manual page for mia-3dmaskseeded, and it lives in section 1 (General Commands Manual), which is where all the user-facing commands hang out. it's giving "I segment things and I do it fabulously." let's get into it 🫶

✨ NAME ✨

mia-3dmaskseeded — mask an area by seeded region growing. literally what it says on the tin, no cap 💅

✨ SYNOPSIS ✨

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

✨ DESCRIPTION ✨

so here's the vibe: mia-3dmaskseeded does 3D image segmentation based on region growing from a seed point. think of the seed as the main character and all its neighbors as the group chat it keeps adding to 👑

neighboring points get added when either:

  • their intensity is equal to or higher than the seed point's intensity, OR
  • their intensity is lower than or equal to that of the neighboring point

once the region growing is all done, that mask gets used to zero out the region in the original image, and that's how you get your resulting image. iconic behavior, truly 🌈

✨ OPTIONS ✨

  • -i, --in-file=(input, required); io — the input image(s) to be filtered. for the supported file types, go peek at PLUGINS:3dimage/io 📂
  • -o, --out-file=(output, required); io — the output image(s) that have been filtered. supported file types are also over at PLUGINS:3dimage/io 💾
  • -s, --seed=[0,0,0] — the seed point 🎯
  • -n, --neighborhood=6n — neighborhood shape. supported plugins live at PLUGINS:3dimage/shape 🧩

🎀 Help & Info 🎀

  • -V, --verbose=warning — verbosity of output; prints messages of the given level and higher priorities. the 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 — maxiumum number of threads to use for processing. (yes, "maxiumum", the original said it like that, and we respect the original ✋) this number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

✨ PLUGINS: 3dimage/io ✨

all the little file-format besties that can slide in and out 💖

  • 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
bestie, note that mhd, vti and vtk are flagged (experimental) — the original said it, so I'm saying it, that's the rules 💀

✨ PLUGINS: 3dimage/shape ✨

your neighborhood shape options 🔮

  • 18n — 18n neighborhood 3D shape creator
    • (no parameters)
  • 26n — 26n neighborhood 3D shape creator
    • (no parameters)
  • 6n — 6n neighborhood 3D shape creator
    • (no parameters)
  • sphere — closed spherical shape neighborhood including the pixels within a given radius r. supported parameters are:
    • r = 2; float in (0, inf) — sphere radius.

✨ EXAMPLE ✨

run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood:

mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

ate. no crumbs. 🍓

✨ 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'. 🫶📜

okay that's the whole page, bestie!! stay slay, mask responsibly 💅

USER COMMANDS · v2.4.7 · mia-3dmaskseeded(1) — mwah, go segment something gorgeous 🌸🦋

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