overlap(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ overlap(1) — The Computational Morphometry Toolkit ✨

okay bestie, so you know the CMTK toolkit? this is one of its little icons, overlap, living in section 1 of the manual. let's get into it 💖

🌸 NAME 🌸

overlap — overlap computation, like, literally just computing overlap. that's the whole vibe.

🦋 SYNOPSIS 🦋

overlap [options] image0 image1 [image2 ...]

💜 DESCRIPTION 💜

so what does it DO? it computes overlap measures between two or more images. that's it, that's the girlboss job. give it a stack of images, get overlap numbers back. no cap. ✨

👑 OPTIONS 👑

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

these ones are the communal wardrobe — every CMTK tool wears them, not just overlap. periodt.

  • --help — writes the list of basic command line options to standard output. baby's first flag 🍼
  • --help-all — writes the complete list of basic AND advanced command line options to standard output. the full lore drop, no secrets kept.
  • --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, it can generate pages like this one. self-referential icon behaviour 💅
  • --version — writes the toolkit version to standard output. who are you? what year is it? found out here.
  • --echo — writes the current command line to standard output. it repeats your own words back at you. very demure, very mindful.
  • --verbose-level <integer> — sets the verbosity level. pick your yap level, 1 to max.
  • --verbose, -v — increments the verbosity level by 1. ⚠️ deprecated; supported for backward compatibility. still slaying, just... retro slaying.
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). let her multitask 🧚

💖 Main Options 💖

the actual main-character flags, the ones that do the overlap thing:

  • --pad-in <double>, -p <double> — define the padding value for input images. [Default: disabled]
  • --mask <string>, -m <string> — mask file for optional region-based analysis. [Default: NONE]
  • --num-labels <integer>, -N <integer> — number of label values. [default: autodetect] [Default: 0]
  • --first-label <integer>, -f <integer> — index of the first label value. [default: 0]; labels below this one are ignored. [Default: 0]
  • --by-label — analysis by label, i.e. separately for each label in the given (detected) range. one label at a time, she's focused ✨

🎀 AUTHORS 🎀

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. the whole squad, credited, as they should be 💜

📜 LICENSE 📜

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

💀 BUGS 💀

report bugs at http://nitrc.org/projects/cmtk/. not me gatekeeping the bug tracker, go tell them everything 🙈

🌟 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, respectfully acknowledged 🫶

and that's the page, bestie — brought to you by CMTK 3.3.1p2, dated Jun 24 2026. go compute some overlap, you've got this 💅✨🌸

📦 where this page comes from