similarity(1)

✨ similarity(1) — The Computational Morphometry Toolkit ✨

okay bestie, sit DOWN, because we're about to talk about similarity, a lil CMTK tool that lives in your terminal and is genuinely so good at comparing two images 💖 it's giving "matchmaker but for brain scans" and honestly? iconic.

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🌸 NAME 🌸

similarity — Image similarity 💅 like, it compares. that's the whole vibe.

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🎀 SYNOPSIS 🎀

similarity Image0 Image1

two images in, one similarity measure out, no cap. 🦋

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💖 DESCRIPTION 💖

bestie. what this does is compute similarity measures between two images — think intensity difference, or label overlaps if your pixels are labels instead of intensities. you hand it two images and it tells you how alike they are. that's it, that's the whole thing, and the way that it just works?? obsessed. ✨

fr fr, this is the main character of the whole page. no shame in that.

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✨ OPTIONS ✨

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

these ones are the universal besties — every CMTK tool has them, so once you learn them you're basically set for life 🫶

• --help — writes the list of basic command line options straight to standard output. baby's first flag 💕
• --help-all — writes the complete list of basic AND advanced command line options to standard output. deep dive mode, we're reading the whole lore 🧚
• --wiki — writes the list of command line options to standard output in MediaWiki markup. yes, for the wiki girlies.
• --man — writes man page source in nroff markup to standard output. meta?? on a man page?? literally yes.
• --version — writes the toolkit version to standard output. we're checking the vibe. 👑
• --echo — writes the current command line to standard output. it just repeats your whole command back at you like "heard u the first time" 😭
• --verbose-level <integer> — set the verbosity level. dial it up, dial it down, integer style.
• --verbose, -v — increment verbosity level by 1. ⚠️ heads up bestie: this one is deprecated — it's only still around for backward compatibility, so don't build anything new on it.
• --threads <integer> — set the maximum number of parallel threads (for POSIX threads and OpenMP). more threads = more chaos = more speed, within reason 🌈

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🔥 Main Options 🔥

this is where the actual similarity gossip happens:

• --outside-bg — assume voxels outside the floating image are background. ok so the floating image is the one being floaty about things 🦋
• --pad0 <double> — define the padding value for the reference image. [Default: disabled]
• --pad1 <double> — define the padding value for the floating image. [Default: disabled]
• --grey, -g — image pixels are intensities. [This is the default] so if you don't say anything, this is what you get 🎀
• --labels, -l — image pixels are labels. switch over here when you're doing label overlap biz 💅
• --mask <string>, -m <string> — mask file for optional region-based analysis. [Default: NONE]
• --force-max <integer> — force the maximum label value. [Default: 0]
• --histogram-text-file <string> — output file name for the histogram (plain text format). [Default: NONE]

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👑 AUTHORS 👑

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko.

the whole squad showed up and honestly they ate 💜

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🎀 LICENSE 🎀

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

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💀 BUGS 💀

found a bug? report bugs at http://nitrc.org/projects/cmtk/ — do NOT sit on it, we're telling the internet fr fr 🙈

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🌈 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.

the way that funding history got its OWN paragraph?? respect the receipts. 💜

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okay pookie, that's the whole page 🦋 you're now officially certified in similarity(1) and nobody can take that from you. this bad girl is CMTK 3.3.1p2, dated Jun 24 2026, and yeah — it still calls itself similarity(1) at the bottom like the icon it is. slay, periodt, go compare some images 💅✨