gmm(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 gmm — Gaussian Mixture Model Segmentation 💖

okay so bestie, this is gmm(1) from The Computational Morphometry Toolkit (that's CMTK to the girlies who know 💅) and it's literally the girlboss of brain-image segmentation. Let's get into it ✨

🌸 NAME 🌸

gmm — Gaussian mixture model segmentation. that's it, that's the whole vibe 🎀

🦋 SYNOPSIS 🦋

gmm InputImage OutputImage PriorImages

three little args and she's ready to slay 💖

✨ DESCRIPTION ✨

So what she actually does: you hand her an image and she segments it into c classes using the EM algorithm for Gaussian mixtures, with optional priors if you're feeling fancy. that's the whole thing. no notes. 🔥

👑 OPTIONS 👑

🌈 Global Toolkit Options (these are shared by all CMTK tools)

these ones are the communal property of every CMTK tool, so you'll see them everywhere. iconic behavior honestly.

  • --help — writes the list of basic command line options to standard output. the starter pack 🫶
  • --help-all — writes the complete list of basic and advanced command line options to standard output. the deluxe edition, the director's cut, the full lore ✨
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. for when you're feeling wiki-pilled 📝
  • --man — writes man page source in 'nroff' markup to standard output. manpage-ception fr fr 💀
  • --xml — writes command line syntax specification in XML markup (this one's for Slicer integration, iykyk) 🧩
  • --version — writes the toolkit version to standard output. flex the number bestie 💅
  • --echo — writes the current command line to standard output. so you can see exactly what you just did 🙈
  • --verbose-level <integer> — sets the verbosity level. turn that dial, girl 🎚️
  • --verbose, -v — increments the verbosity level by 1. ⚠️ deprecated, but supported for backward compatibility — she's an old queen and we respect her, but maybe don't build your whole life on her 💜
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). make her run in parallel, she loves that 🏃‍♀️💨

🍓 General Classification Parameters

the actually-important girlies for this specific tool:

  • --mask <string>, -m <string> — path to the foreground mask image. if you don't provide one, the input image gets used as its own mask — but that does NOT work properly if the input image itself has pixels with zero or negative values. so like... heads up bestie 😭 [Default: NONE]
  • --classes <integer>, -c <integer> — number of classes. how many buckets are we sorting into, queen? [Default: 3]
  • --iterations <integer>, -n <integer> — number of EM iterations. how many times she loops that EM glow-up routine. [Default: 10]

🧚 Handling of Priors

for when you come bearing prior knowledge (a gift, honestly):

  • --priors-init-only — use priors for initialization only. one-and-done, she doesn't keep consulting them 🎀
  • --prior-epsilon <double>, -e <double> — a small value added to all class priors to eliminate zero priors. tiny little epsilon, doing the lord's work so nothing ends up at zero 🙏 [Default: 0]

💅 Output Parameters

  • --probability-maps, -p — write probability maps. the file names for these maps get generated from the output image path by inserting '_prob#' before the file format suffix, where '#' is the index of the respective class, numbered starting at 1 (zero is background). so yes, class numbering starts at 1 here, background owns the zero, don't @ me 🌈

💜 AUTHORS 💜

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. a whole squad, a whole ensemble cast, and they ate 👑

📜 LICENSE 📜

http://www.fsf.org/licensing/licenses/gpl.html

GPL things, go read it, it's giving freedom 🕊️

💀 BUGS 💀

Report bugs at:

http://nitrc.org/projects/cmtk/

not me asking you to file a bug report but like... please do, she wants to be fixed 🙈

🌟 ACKNOWLEDGMENTS 🌟

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.

shoutout to the funders, real ones fr fr 💖

aaand that's the whole page bestie! this is CMTK 3.3.1p2, dated Jun 24 2026 — she's current, she's cute, she segments. go forth and cluster ✨🦋🎀💅

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