mia-2dseriestovolume(1)

📦
version 2.4.7 · 2 versions
, in ubuntu jammy, ubuntu resolute, ubuntu stonking

💖 mia-2dseriestovolume — like, the manual page, bestie 💖

okay so you found the mia-2dseriestovolume(1) page, and it lives in the General Commands Manual section, and I'm gonna walk you through the whole thing like we're texting at 2am. buckle up. 🎀

✨ NAME ✨

mia-2dseriestovolume — Create a 3D volume from a segmentation series.

that's it, that's the whole vibe. it takes your lil stack of 2D segmentation slices and glues them into one iconic 3D volume. no cap. 👑

🌸 SYNOPSIS 🌸

mia-2dseriestovolume -i <in-file> -o <out-file> [options]

in goes the series, out comes the volume, and everything else is optional sprinkles. 💅

🦋 DESCRIPTION 🦋

mia-2dseriestovolume Obtaines a 3D volume image by combining the images of the segmentation set.

literally that's the whole thing. you hand it the set, it stacks the frames, you get a 3D image at the end. it's giving "assembly line but make it ✨anatomy✨". the way that it just… combines them — obsessed. 🫶

💅 OPTIONS 💅

  • -i --in-file=(input, required); string — the input segmentation set. required, girl, it will not read your mind.
  • -o --out-file=(output, required); io — the output 3D image.
    • For supported file types see PLUGINS:3dimage/io (scroll down, it's literally right there ⤵️)
  • -k --skip=0 — number of frames to skip at the beginning of the series. defaults to 0, so by default we take everything. 🌈

🎀 Help & Info 🎀

  • -V --verbose=warning — verbosity of output, print messages of given level and higher priorities. defaults to warning. 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

lowest level = most yapping, highest level = only the dire stuff, iykyk.

  • --copyright — print copyright information. 🫶
  • -h --help — print this help. your bestie when you forget a flag.
  • -? --usage — print a short help. the tl;dr version.
  • --version — print the version number and exit. it tells you who it is and then dips. 💀

🔥 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).
girl, read the room: don't set this higher than your actual logical cores. and yes the original says "Maxiumum", we're keeping it ✨verbatim✨ because the facts stay, even when the typo is cute. -1 = it figures it out itself, main character energy. 👑

🧚 PLUGINS: 3dimage/io 🧚

these are all the file formats the 3D image IO can vibe with, bestie. every single one, no skipping. 💖

  • 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
heads up bestie: mhd, vti and vtk are marked (experimental) in the original. slay, but proceed knowing that. 💀✨

🍓 EXAMPLE 🍓

Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

see how -k 2 just tosses the first two frames? chef's kiss. into series.set, out comes volume.v, done. 🎀

💜 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'.

say it with me: ABSOLUTELY NO WARRANTY. it's giving "free software, free as in freedom, not as in free tech support". 💅

okay that's the whole page, you're officially educated, go make a 3D volume, and remember: this is mia-2dseriestovolume(1) from the USER COMMANDS section, version v2.4.7. mwah. 💖🌈🦋🫶

📦 where this page comes from