mia-3dimagestats(1)

📦
version 2.4.7 · 2 versions
, in debian bookworm, ubuntu jammy, ubuntu noble

💖 mia-3dimagestats(1) 💖

okay bestie, welcome to the General Commands Manual entry for mia-3dimagestats — she's a little console gremlin who reads your 3D images and spills their stats to the terminal. no cap. 🎀

✨ NAME ✨

mia-3dimagestats — Evaluate some image statistics.

like... she just looks at your image and tells you the numbers. iconic behaviour honestly. 📊

🌸 SYNOPSIS 🌸

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

🦋 DESCRIPTION 🦋

mia-3dimagestats is the program you run when you want to evaluate certain image statistics and print them out on the console. that's it. that's the whole job. she computes, she prints, she leaves. main character energy, minimal screen time. 💅

👑 OPTIONS 👑

  • -i, --in-file=(required, input); io — the input image(s) to be filtered. yes bestie it's required, so don't ghost her on this one. 🙈
    • For supported file types see PLUGINS:3dimage/io
  • -t, --thresh=10 — intensity thresh to ignore. anything below this vibe check gets skipped. default is 10.

🌈 Help & Info 🌈

  • -V, --verbose=warning — verbosity of output, prints messages of given level and higher priorities. default is warning. Supported priorities, starting at the lowest level, are:
    1. trace ‐ Function call trace
    2. debug ‐ Debug output
    3. info ‐ Low level messages
    4. message ‐ Normal messages
    5. warning ‐ Warnings
    6. fail ‐ Report test failures
    7. error ‐ Report errors
    8. fatal ‐ Report only fatal errors
  • --copyright — print copyright information. the legal tea. ☕
  • -h, --help — print this help.
  • -?, --usage — print a short help. the lite version, for when you're in a rush.
  • --version — print the version number and exit. she'll tell you her age and then dip. 👋

🔥 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). so like, if you put a number bigger than your cores she will simply be overstimulated. don't do that to her. 🫶

🧚 PLUGINS: 3dimage/io 🧚

here's the full roster of file formats she fw, with every extension and every element type, no gatekeeping:

  • 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
ngl a couple of these are marked (experimental), so treat them like a situationship: cute, fun, but maybe don't build your whole pipeline on them. 💀

💜 EXAMPLE 💜

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

see? one line and she's already doing the most. periodt. ✨

🍓 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.

bestie read this part fr fr — no warranty, like zero, none, nada. it's GPL v3 or later, so share the love, not the liability. 🫶

and that's a wrap on mia-3dimagestats! this page came from the USER COMMANDS section, v2.4.7 — go off, have fun computing your stats, and remember: thresh responsibly. mwah 💅✨💖

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