make_i..._affine(1)

✨ make_initial_affine — bestie edition 💖

okay so you opened the manual page for make_i..._affine(1) — yes that's section 1 of the man pages, the whole CMTK thing — and honestly? you've come to the right place. sit down, hydrate, let's get you an affine transformation. 🫶

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🌸 NAME 🌸

make_initial_affine — Initialize affine transformation ✨

🎀 SYNOPSIS 🎀

make_initial_affine ReferenceImage FloatingImage OutputXform

that's it. three little args. three. you got this. 💅

🦋 DESCRIPTION 🦋

Compute initial affine transformation by aligning centers of mass or principal axes 🧚

like, the vibe is: we don't know exactly how these two brain images line up yet, but we can get a first guess going. and a first guess is honestly all you need to start the real registration. it's giving "let me just get us in the right ballpark" energy. 👑

🌈 OPTIONS 🌈

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

these ones are the communal wardrobe, bestie — every CMTK tool has them, not just this one.

• --help — drops the list of basic command line options straight to standard output. your lil cheat sheet. 📝
• --help-all — same but everything, basic and advanced options, all of it, to standard output. 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 the man page source in 'nroff' markup to standard output. meta? lowkey meta. 🌀
• --xml — writes the command line syntax specification in XML markup (yes, for Slicer integration). 🧩
• --version — writes the toolkit version to standard output. identity reveal moment. 💫
• --echo — writes the current command line to standard output. like a mirror for your terminal. 🪞
• --verbose-level <integer> — sets the verbosity level. crank it up, hear everything. 🔊
• --verbose, -v — increments verbosity level by 1. deprecated though — it's only still around for backward compatibility. it's an icon but it's retired, no cap. 💀
• --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). make it go fast, bestie. 🔥

💜 Transformation construction control 💜

this is the main character section of this whole manpage, fr fr.

• --mode — Mode selection for initialization. Supported values: "direction-vectors", "centers-of-mass", "principal-axes", "identity", where the default is "direction-vectors", or use one of the following:
  • --direction-vectors — Alignment based on image direction vectors. [This is the default] ⭐
  • --centers-of-mass — Alignment based on centers of mass (translation only) 🫶
  • --principal-axes — Alignment based on principal axes 📐
  • --identity — Create only an identity transformation. sometimes doing nothing is the move. 🙈
• --center-xform, -C — Set transformation center (for rotation, scale) to center of reference image. 🎯
• --native-space — Write transformation between the native image spaces, rather than in CMTK standard RAS space. This is the default when running this tool as a Slicer plugin. 🧚

🍓 Image/Transformation Database 🍓

• --db <string> — Path to image/transformation database that should be updated with the newly transformation from reference to floating image. [Default: NONE] 💾

icymi: the default for --db is NONE, so if you don't say anything, nothing gets written to a database. just so you know. 💖

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🌟 AUTHORS 🌟

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko 👑👑👑 absolute legends, every single one.

💜 LICENSE 💜

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

🩹 BUGS 🩹

Report bugs at http://nitrc.org/projects/cmtk/ — they want to hear from you, bestie, it's not a bother, it's a contribution. 🫶

🌈 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. 🙏✨

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okay and that's the whole thing!! this page is from CMTK 3.3.1p2, dated Jun 24 2026, and yeah — footer energy, but make it cute. go get that initial affine, bestie, you're gonna slay it. 💅🎀🦋