mia-3dcomb...mentations(1)

💖 mia-3dcombine-mr-segmentations — bestie edition 💖

okay so real quick: this page lives in the General Commands Manual, section 1, and the whole thing is called mia-3dcomb...mentations (the name got a lil truncated, she's mysterious like that 🎀). Anyway. Sit down, grab a snack, we're combining segmentations and it's gonna be adorable. ✨

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✨ NAME ✨

mia-3dcombine-mr-segmentations — Combine segmentations. that's it. that's the girl. 💅

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🦋 SYNOPSIS 🦋

mia-3dcombine-mr-segmentations -i <in-file> -o <out-file> [options]
<PLUGINS:3dimage/io>

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🌸 DESCRIPTION 🌸

okay so picture this: you've got a bunch of segmentation masks of the same data, plus a tissue probability image set, and you want them all smooshed together into one single labeled image. That's literally her whole job. 👑

Here's the tea on how the labels get assigned: the masks are translated to labels according to the position on the command line. So order matters, bestie — don't be out here shuffling your arguments like it's a playlist. 🙈

And if a voxel gets flagged as belonging to more than one mask? Not a problem, she doesn't panic. The probabilities get consulted and they sort it out amongst themselves. very mature of them honestly. 🌈

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💜 OPTIONS 💜

• -i, --in-file=(required, input); io — your input probability images. The number of mask images must correspond to the number of probability images you hand over here. Match them up, no cap. For supported file types see PLUGINS:3dimage/io 🫶
• -o, --out-file=(required, output); io — the output image that contains the labeling. Your masterpiece. Your final girl. For supported file types see PLUGINS:3dimage/io 💖

🎀 Help & Info 🎀

• -V, --verbose=warning — verbosity of output, print messages of given level and higher priorities. 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
• --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, This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

ngl the original spells it "Maxiumum" and I'm keeping it, that's a historical artifact, we respect the ancestors. 💀

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🔥 PLUGINS: 3dimage/io 🔥

all the file formats she can vibe with, in alphabetical order, no crumbs left behind:

• 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 ⭐

mia-3dcombine-mr-segmentations

iconic. no arguments. just vibes. ✨

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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.

fr fr: no warranty. like, none. zero. she said what she said. 💅

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okay that's the whole page bestie, you're officially educated 💖 this little cutie is a USER COMMAND page, version v2.4.7, and yes she really does spell her own name mia-3dcomb...mentations with the dots — queen of mystique 🎀✨ mwah, go combine some segmentations, you got this 🫶