mia-3dbrainextractT1(1)

🧠 mia-3dbrainextractT1 — the brain-extraction bestie 🧠

okay so bestie, welcome to the General Commands Manual page for mia-3dbrainextractT1, and honestly? it's giving neuroimaging main character energy. it pulls the brain out of a 3D T1 MRI head image. yes, literally. no cap. 🧠✨

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🌸 SYNOPSIS 🌸

mia-3dbrainextractT1 -i <in-file> -o <out-file> [options]

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💖 DESCRIPTION 💖

okay so here's the tea: mia-3dbrainextractT1 is the program you use to extract the brain from T1 MR images. 🧠💅

the way it works is honestly iconic — first it runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of a 3D image. then various fiters are run to obtain a white matter segmentation as an initial mask, and that mask is then used to run a region growing to obtain a mask of the whole brain. finally, this mask is used to extact the brain from the B0 field corrected images. 🎀

like… it's a whole pipeline and it ate. periodt.

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✨ OPTIONS ✨

🫶 the main ones 🫶

• -i, --in-file=(input, required); io — the input image(s) to be segmented, bestie. you gotta give it this one. for supported file types see PLUGINS:3dimage/io 👇
• -o, --out-file=(output, required); io — this is your brain mask output. also required, no skipping. for supported file types see PLUGINS:3dimage/io 👇
• -n, --no-of-classes=3 — number of classes. default is 3 🎚️
• -w, --wm-class=2 — index of white matter. default is 2 🧠
• -p, --wm-prob=0.7 — white matter class probability for initial mask creation. default is 0.7 🌟
• -t, --grow-threshold=20 — intensity threshold for region growing. default is 20 🔥
• --grow-shape=18n — neighbourhood mask region growing. default is 18n 🦋

🫶 Help & Info 🫶

• -V, --verbose=warning — verbosity of output: 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 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). 🏃♀️💨

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🌈 PLUGINS: 3dimage/io 🌈

these are all the file formats it can vibe with, iykyk:

• 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 🍓

Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v:

mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v

like… look at her go. slay. 💅

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👑 AUTHOR(s) 👑

Gert Wollny — the icon, the legend. 🫶

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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'. 📜✨

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and that's the whole page, bestie!! 🎀 this one came to you straight outta the USER COMMANDS section, version v2.4.7, filed under mia-3dbrainextractT1(1). go extract some brains (respectfully) 🧠💖🦋