asegment_sri24(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 asegment_sri24 — bestie, it's the SRI24 atlas segmentation tool 💖

okay so this is asegment_sri24(1), a lil legend from the Computational Morphometry Toolkit (that's CMTK, iykyk 🧠✨). she takes your brain pic and glams it up against the SRI24 human brain atlas like it's getting ready for the met gala.

✨ NAME ✨

asegment_sri24 — literally just: segmentation using the SRI24 atlas. that's the whole vibe. no cap. 🎀

🌸 SYNOPSIS 🌸

asegment_sri24 TargetImage OutputImage

like. two things. in. that's it. periodt. 💅

🦋 DESCRIPTION 🦋

okay so here's the tea ☕: this tool registers your target image to a selected channel of the SRI24 human brain atlas, and then it reformats one of the atlas label maps over onto your target image. so you give it a brain, it gives you back a brained-up brain with atlas labels on it. iconic behavior honestly.

⚠️ heads up bestie: it is assumed that the target image is skull-stripped, i.e., it contains only the brain. no skull. no skull at all. if you leave the skull in, that's on you and the vibes will be off. 😭💀

👑 OPTIONS 👑

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

these are the communal ones, everyone gets them, share the wealth bestie 🫶

  • --help — writes a list of the basic command line options to standard output. the lil starter pack. 🌱
  • --help-all — writes the complete list, basic AND advanced, to standard output. the deluxe version. the whole closet. 👗
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. for when you need it wiki-fied. 🧚
  • --man — writes man page source in 'nroff' markup to standard output. yes, it prints its own manpage. recursive slay. 🔁
  • --xml — writes command line syntax specification in XML markup (for Slicer integration). it's giving ✨ structured ✨.
  • --version — writes toolkit version to standard output. so you know exactly which queen you're talking to. 👑
  • --echo — writes the current command line to standard output. receipts, always. 🧾
  • --verbose-level <integer> — set verbosity level. give it a number, bestie.
  • --verbose, -v — increment verbosity level by 1. > ⚠️ deprecated — it's only still here for backward compatibility, so she's basically in her retirement era. still works tho. 🙈
  • --threads <integer> — set maximum number of parallel threads (for POSIX threads and OpenMP). more threads = more girlies working at once. 💪

🔥 Main Options 🔥

  • --fast, -f — Fast mode. zoom zoom. ⚡
  • --registration-channel — this is the SRI24 channel used for registration to the target image. supported values: "spgr", "early-fse", "late-fse", "fa", and the default is "spgr". or you can use one of these individually instead:
    • --spgr — SPGR (T1-weighted) structural channel. [This is the default] ⭐
    • --early-fse — Early-echo (PD-weighted) fast spin echo channel. 🍓
    • --late-fse — Late-echo (T2-weighted) fast spin echo channel. 🌸
    • --fa — Fractional anisotropy channel, derived from diffusion tensor images. the DTI girly. 🧠✨
  • --label-map — this is the SRI24 label map that gets reformatted to the target image. supported values: "tzo116plus", "lpba40", "tissue", and the default is "tzo116plus". or use one of these on their own:
    • --tzo116plus — Extended cortical parcellation template based on Tzourio-Mazoyer AAL 116 region template. [This is the default] ⭐
    • --lpba40 — Template based on the 40 subject LONI Probabilistic Brain Atlas segmentation. forty whole subjects, no cap. 🫶
    • --tissue — SRI24 maximum likelihood three compartment (GM, WM, CSF) tissue segmentation map. three compartments, three moods. 💅

💜 AUTHORS 💜

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. a whole squad, we love a collab. 🌈✨

📜 LICENSE 📜

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

🐛 BUGS 🐛

Report bugs at http://nitrc.org/projects/cmtk/

(be nice to them, they're doing their best 🥺)

🎀 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 queens, we stan. 👑

and that's the whole page bestie!! 🎉 this ran under CMTK 3.3.1p2, dated Jun 24 2026 — write it in your notes, screenshot it, tattoo it, whatever. go strip some skulls and segment some brains. you got this. 💖✨🦋

📦 where this page comes from