avg_adm(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

🎀 NAME 🎀

avg_adm — Average using ADM

okay so you've pulled up avg_adm(1), one of the tools from The Computational Morphometry Toolkit (CMTK), and honestly? she's a baddie 💖. here's the whole rundown, no gatekeeping.

✨ SYNOPSIS ✨

avg_adm [options] list0 [list1 ...]

that's it. you pass it some lists, you give it options, she does her thing 🫶

🦋 DESCRIPTION 🦋

avg_adm computes average-shape average-intensity images and deformation maps using an active deformation model. that's the whole vibe — shape averaging + intensity averaging + the deformation maps, all in one, powered by ADM. 🧚 periodt.

💅 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 set for life, iykyk.

  • --help — writes the list of basic command line options to standard output. the "just tell me the essentials" button.
  • --help-all — writes the complete list of basic and advanced command line options to standard output. the full lore, no crumbs withheld 🔥
  • --wiki — writes the list of command line options to standard output in MediaWiki markup.
  • --man — writes the man page source in nroff markup to standard output.
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output. (look at her, repeating you back to yourself 💀)
  • --verbose-level <integer> — sets the verbosity level.
  • --verbose, -v — increments verbosity level by 1. it's deprecated, but supported for backward compatibility, so she's still here for the old school crowd 🫡
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). more threads = more chaos = faster, bestie.

💖 Main Options 💖

the actual main character options. here we go:

  • --label, -l — Label mode (as opposed to grey). pick this when your data is labels, not greyscale vibes.
  • --set-padding <float> — sets the padding value in input files [Default: disabled]. she's off until you turn her on.
  • --replace-padding <float> — replaces the padding value in input files [Default: disabled]. yeah, different from set — read the words, bestie.
  • --pad-out <double>, -p <double> — the padding value for the output file [Default: disabled].
  • --jacobian, -j — average Jacobian determinants of deformations. math girlies rise ✨
  • --auto-scale, -a — auto-scale image intensities.
  • --char — output is 8 bits, signed [default: automatic].
  • --byte — output is 8 bits, unsigned.
  • --short — output is 16 bits, signed.
  • --ushort — output is 16 bits, unsigned.
  • --int — output is 32 bits signed.
  • --float — output is 32 bits floating point.
  • --double — output is 64 bits floating point. double the bits, double the drama 💅
  • --no-scale-model, -S — exclude scale from the statistical deformation model.
  • --no-ref-model, -R — exclude the reference coordinate frame from the deformation model.
  • --no-ref-data, -r — exclude reference data from averaging.
  • --output <string>, -o <string> — output file name, in the form [FORMAT:]path [Default: NONE]. yes the format prefix is optional, and yes you should probably use it.
  • --input-warp <string>, -I <string> — input file name for the average warp [Default: NONE].
  • --output-warp <string>, -O <string> — output file name for the average warp [Default: NONE].
  • --with-affine, -A — include the affine component of the first warp in the output.
  • --nn — use nearest neigbor interpolation. (that's "neighbor" — the spelling is just like that, ok, we don't judge 💀)
  • --cubic — use tri-cubic interpolation.
  • --replace-from <string> — the replace-from pattern.
  • --replace-to <string> — the replace-to pattern. (they're a matching set, obvi 🎀)

🌈 AUTHORS 🌈

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. the whole squad, legendary lineup, we stan 👑

📜 LICENSE 📜

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

🐛 BUGS 🐛

found a bug? report it at http://nitrc.org/projects/cmtk/ — don't 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 page, you ate that 🍓 this was CMTK 3.3.1p2, dated Jun 24 2026, signing off with main character energy — go average something iconic, bestie 💖✨👑

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