average_images(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ average_images — NAME 💖

okay so average_images is literally THE girl for averaging images 💅 — it's a CMTK tool (The Computational Morphology Toolkit, iykyk) and it eats a whole list of images for breakfast and hands you back the math-y version of them.

🌸 SYNOPSIS 🌸

average_images [options] image0 ...

like. you hand her a bunch of image0 ... files, you sprinkle options on top, she does her thing. so simple. so iconic. 🫶

🦋 DESCRIPTION 🦋

bestie listen. this tool computes pixelwise average, variance, standard deviation, z-score, or entropy images from a list of intensity images you provide. that's it, that's the whole job, and she does it flawlessly no cap. ✨

👑 OPTIONS 👑

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

every CMTK tool gets these, they're like the group chat everyone's in:

  • --help — writes the list of basic command line options to standard output. your lil starter pack 🎀
  • --help-all — writes the COMPLETE list of basic and advanced command line options to standard output. the full lore, the extended cut 💀
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. for the wiki girlies 🌈
  • --man — writes man page source in 'nroff' markup to standard output. yes, the very format you're reading rn, meta ik 😭
  • --version — writes the toolkit version to standard output. vibe check the version ✨
  • --echo — writes the current command line to standard output. she repeats you back, respectfully 🫶
  • --verbose-level <integer> — sets the verbosity level. pick a number, any number 📢
  • --verbose, -v — increments the verbosity level by 1. > ⚠️ heads up: this one is deprecated; it's only supported for backward compatibility. she's still here for you but she's lowkey retired 💀
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). more threads = more chaos = go faster 🔥

🌸 Main Options 🌸

  • --mode — the mode of averaging operation. supported values: "avg", "var", "stdev", "zscore", "entropy", where the default is "avg". or, alternatively, just use one of these cuties:
    • --avg — compute average (i.e., mean) image. [This is the default] ✨
    • --var — compute variance image.
    • --stdev — compute standard deviation image.
    • --zscore — compute z-score image.
    • --entropy — compute pixel-by-pixel population entropy image. the chaotic one, obsessed 🌀

🎀 Data Preprocessing 🎀

get your data cute before she averages it:

  • --log, -l — apply log to input data. math-ify it first 📐
  • --abs, -a — use absolute input values. no negatives allowed, periodt ✋
  • --normalize-mean-stdev, -n — normalize image intensities using means and standard deviations. gets everyone on the same playing field 💅
  • --set-padding-value <double> — define padding value in input images. [Default: disabled] — so by default there's no padding value set at all, fr fr 🫥

💖 Output Options 💖

  • --outfile-name <string>, -o <string> — output file name. [Default: average.nii ]
  • --type — scalar data type of output image. supported values: "float", "double", where the default is "float". or use one of these:
    • --float — single-precision float. [This is the default] ✨
    • --double — double-precision float. she's extra precise, she's built different 👑

🫶 AUTHORS 🫶

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

tag yourself, I'm the entire contributor list 💜

📜 LICENSE 📜

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

🐛 BUGS 🐛

found a bug? report bugs at http://nitrc.org/projects/cmtk/ — do NOT suffer in silence bestie, tell the devs 😭

🌟 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.

and that's the whole thing 💖 go average some images, you absolute icon, I'm so proud of you 🫶✨

this has been your girl from CMTK 3.3.1p2, dated Jun 24 2026, signing off — slay, bye 👑💅

📦 where this page comes from