epiunwarp(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💅 epiunwarp — the manual, but make it make sense 🧚

okay so this is epiunwarp, bestie, and it lives in The Computational Morphology Toolkit (yes, that's CMTK, we're fancy here 👑). It's the little tool that un-squishes your Echo Planar Images. Grab a snack, we're going in 🍓

✨ NAME ✨

epiunwarp — Unwarp Echo Planar Images. That's it, that's the whole vibe. 🌈

🦋 SYNOPSIS 🦋

epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField
OutputDFieldRev

Six arguments, in that exact order, no cap. Two go in, four come out. It's giving ✨pipeline✨.

💖 DESCRIPTION 💖

So here's the tea 🫖 — B0 field inhomogeneity is out here causing distortion in Echo Planar Images (think diffusion-weighted images, you know the ones). epiunwarp fixes that up. How? You feed it two images that were acquired with opposing phase encoding directions, and it does the unwarping magic. Two opposing acquisitions, one corrected result. Obsessed. 😭💕

🎀 OPTIONS 🎀

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

Like, every single CMTK tool has these. They're the friend group of options. 💜

  • --help — writes the list of basic command line options to standard output. Your starting point, bestie.
  • --help-all — writes the complete list of basic and advanced command line options to standard output. The full lore. 📚
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. For when you need it wiki-ified.
  • --man — writes man page source in 'nroff' markup to standard output. Manpage-ception. 🌀
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output. It's repeating you back to yourself. iconic behavior.
  • --verbose-level <integer> — set the verbosity level. You control how much it yaps. 🗣️
  • --verbose, -v — increments the verbosity level by 1. ⚠️ Heads up: this one is deprecated — it's only supported for backward compatibility, so don't build your whole personality around it.
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). Go parallel, go fast, go girl. 🔥

🌼 Input Image Parameters

  • --phase-encode — defines the phase-encoded image coordinate direction. Supported values are "phase-encode-ap", "phase-encode-is", and "phase-encode-lr", where the default is "phase-encode-ap". OR, alternatively, you can just use one of these bad boys directly:
    • --phase-encode-ap, -y — Anterior/posterior phase encoding (this is the most common case). [This is the default]
    • --phase-encode-is, -z — Top/bottom phase encoding (this is rare 👀).
    • --phase-encode-lr, -x — Lateral, left/right phase encoding (this is extremely rare, like finding a good avocado rare).
  • --no-flip — use this switch if the reverse phase-encoded image does not need to be flipped prior to unwarping. Here's the test: if the normal and reverse phase-encoded images display in the same gross orientation in triplanar, then flipping is not necessary and must be turned off using this switch. So like, look first, then decide. No guessing 🙈

⭐ Optimization Parameters

  • --no-init-shift-com — disables initialization of unwarping by shifting each row to align the centers of mass of forward and reverse acquisition. Instead, it uses an all-zero initial deformation field. Sometimes you start from zero, sometimes you start from center-of-mass. Character development either way. 💅
  • --smooth-sigma-max <double> — maximum image smoothing kernel width for the coarsest level of the multi-scale computation. [Default: 8]
  • --smooth-sigma-min <double> — minimum image smoothing kernel width for the finest level of the multi-scale computation (0 = no smoothing; original image scale). [Default: 0]
  • --smooth-sigma-diff <double> — the difference between image smoothing kernel widths between two successive levels of the multi-scale computation. [Default: 0.25]
  • --smoothness-constraint-weight <double> — weight factor for the second-order smoothness constraint term in the unwarping cost function. [Default: 0]
  • --folding-constraint-weight <double> — weight factor for the folding-prevention constraint term in the unwarping cost function. [Default: 0]
  • --iterations <integer>, -i <integer> — number of L-BFGS optimization iterations (per multi-scale level). [Default: 10]

🦄 Output Options

  • --write-jacobian-fwd <string> — write the Jacobian intensity correction map for the forward image. [Default: NONE]
  • --write-jacobian-rev <string> — write the Jacobian intensity correction map for the reverse-encoded image. [Default: NONE]
no cap, the defaults for both Jacobian options are NONE, so if you want those maps you literally have to ask for them. speak up, bestie 🗣️💖

👑 AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. A whole squad, we love a collab. 🫶

📜 LICENSE

http://www.fsf.org/licensing/licenses/gpl.html — go read it, it's important. 💜

💀 BUGS

Report bugs at http://nitrc.org/projects/cmtk/. Found a bug? Tell the devs, don't suffer in silence. 😭

🌟 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 girlies, we appreciate you. 🧚💖

mkay so that's the whole page 💅 it's CMTK 3.3.1p2, dated Jun 24 2026, and it's the epiunwarp(1) manual — now go unwarp something, bestie, you've got this 🌈✨🦋

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