asegment(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 asegment(1) — atlas-based segmentation, bestie edition 💖

okay so you found the asegment page, and honestly? iconic choice. this lives in the The Computational Morphometry Toolkit (CMTK for the girlies who are busy), and it's literally here to do one big beautiful thing: take your target image, line it up with an atlas, and yeet the atlas's labels onto your image. slay.

✨ NAME ✨

asegment — atlas-based segmentation. that's it, that's the whole vibe. 🫶

🦋 SYNOPSIS 🦋

asegment TargetImage AtlasImage AtlasLabels OutputImage

four arguments, no notes. you got this. 💅

🌸 DESCRIPTION 🌸

so here's the tea, bestie. asegment registers a target image to an atlas. the way it does that is affine registration first, and then nonrigid B-spline registration on top of it — so yeah, it's the full glow-up pipeline, not just a quick glance in the mirror. ✨

then, once everything's lined up, it reformats the atlas label map so it lands on your target image. boom. segmentation. you're welcome. 🎀

👑 OPTIONS 👑

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

ngl these ones are the group chat everyone's in — every CMTK tool has them. no gatekeeping here. 💖

  • --help — writes the list of basic command line options to standard output. the "just tell me the basics" button.
  • --help-all — writes the complete list of basic and advanced command line options to standard output. the "no actually, tell me EVERYTHING" button. 🍓
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. wiki girlies rise. 💅
  • --man — writes man page source in 'nroff' markup to standard output. yes, man pages inside man pages, we're incepting ourselves.
  • --xml — writes command line syntax specification in XML markup (for Slicer integration). for when Slicer needs the notes. 🧚
  • --version — writes toolkit version to standard output. proof you're running what you think you're running.
  • --echo — writes the current command line to standard output. like a receipt of everything you typed. 🙈
  • --verbose-level <integer> — sets the verbosity level. crank it up, get more words.
  • --verbose, -v — increments verbosity level by 1. heads up though: this one is deprecated and only supported for backward compatibility. still works, still cute, but the new stuff is what you wanna be on. 😭
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). more threads, more main character energy. 🔥

⭐ Main Options ⭐

  • --fast, -f — Fast mode. zoom zoom. 🦋

💖 AUTHORS 💖

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. literal kings, all of them. 👑

📜 LICENSE 📜

http://www.fsf.org/licensing/licenses/gpl.html — go read it, it's giving GPL. ⭐

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/. not me manifesting zero bugs but still handing you the link just in case. 🌈

🎀 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. funding lore, we love to see it. 💜

reminder bestie: this is asegment, the CMTK tool, manual section 1. shipped as part of CMTK version 3.3.1p2, dated Jun 24 2026. periodt. 💅✨🦋
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