volume_injection(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 volume_injection(1) 💖

okay bestie, this is volume_injection from The Computational Morphology Toolkit — yeah that CMTK, the one that lives in your terminal and eats your afternoon. grab a strawberry drink and let's go 🍓

✨ NAME ✨

volume_injection — Volume injection. that's it, that's the name, short and iconic 💅

🌈 SYNOPSIS 🌈

volume_injection [options] refImage xform0 inImage0 [xform1 inImage1 ...]

so you give it a reference image, then keep handing it little pairs of xform + inImage like you're feeding a very hungry goldfish. the more pairs, the more data it gets to play with 🫶

🦋 DESCRIPTION 🦋

okay so the whole point: you have a bunch of co-registered images that are kind of low-res, and this tool reconstructs a high-resolution volume out of them. the technique is forward volume injection. that's the vibe, that's the whole thing, no cap ✨

👑 OPTIONS 👑

🌸 Global Toolkit Options 🌸 (these are shared by all CMTK tools — yes, all of them, they're family)

  • --help — writes the list of basic command line options to standard output. baby version 💖
  • --help-all — writes the complete list of basic and advanced command line options to standard output. the full lore 🔥
  • --wiki — writes the command line options to standard output in MediaWiki markup. for when you're documenting, bestie 📝
  • --man — writes man page source in 'nroff' markup to standard output. yes, the very thing you're reading, but boring-er 🎀
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output. so you can see what you actually typed 😭
  • --verbose-level <integer> — sets the verbosity level. tell it how chatty to be.
  • --verbose, -v — increments the verbosity level by 1. > heads up: this one is deprecated; it's supported for backward compatibility only. still works, still slays, but iykyk ⭐
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). go off, multicore 👑

🎀 Input Options 🎀

  • --exclude-first-image, -x — excludes the first image from the reconstruction, treating it as a separate registration target image. lowkey the main character gets benched 🙈
  • --pass-weight <string>, -W <string> — sets the contribution weight for a pass, in the form 'pass:weight'. give each pass its own glow-up ✨

💅 Reconstruction Grid Options 💅

  • --recon-grid <string> — defines the reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] — that's dims:pixel:offset, keep that order fr fr 📐
  • --recon-grid-path <string>, -R <string> — gives the path to a grid that defines the reconstructed image grid, including offset. [Default: NONE] 🧚
  • --crop <string> — crops the reference to pixel region x0,y0,z1:x1,y1,z1. yes bestie, that's exactly how it's written. copy it character for character, i am not being weird about it, the manpage is ✂️

🔥 Volume Injection Options 🔥

  • --isotropic-injection — uses isotropic volume injection. [default: scaled with pass image pixel size per dimension] 🌈
  • --injection-kernel-sigma <double>, -S <double> — Gauss contribution. [Default: 1] 🎯
  • --injection-kernel-radius <integer>, -r <integer> — VolumeInjectionRadius of affected pixel. [Default: 0] 💫

🌸 Output Options 🌸

  • --output <string>, -o <string> — output image path. [Default: volume_injection.nii] 💾
  • --write-images-as-float, -F — writes output images as floating point. [default: same as input] 🫶

💜 AUTHORS 💜

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

🎀 LICENSE 🎀

http://www.fsf.org/licensing/licenses/gpl.html — go read it, it's good for you, like vegetables but legally binding 📜

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/. not me manifesting a bug, but if it happens, that's the address 🙈

🦋 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 era, iconic behavior 🫶

and that's the whole page bestie!! this one's from CMTK 3.3.1p2, dated Jun 24 2026 — go reconstruct something gorgeous 💖✨🎀🦋🌸

📦 where this page comes from