xform2dfield(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ xform2dfield ✨

ok so bestie, welcome to the xform2dfield page from the Computational Morphometry Toolkit manual (section 1, iykyk 💅). it's giving "transformation to deformation field" and honestly? it ate. let's get into it 🫶

🎀 NAME 🎀

xform2dfield — Transformation to Deformation Field. that's it, that's the vibe ✨

🌸 SYNOPSIS 🌸

xform2dfield OutputPath ReferenceImage XformList

three args, no notes, iconic 👑

🦋 DESCRIPTION 🦋

okay so here's the tea: this tool converts a parametric rigid or nonrigid transformation into a deformation field, and it samples that field at the pixel locations of a reference image you hand it. that's the whole plot. simple, slay, efficient 💖

💅 OPTIONS 💅

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

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

  • --help — writes the list of basic command line options to standard output. baby's first help, we love her 🎀
  • --help-all — writes the complete list, basic and advanced command line options, to standard output. the full lore drop 😭
  • --wiki — writes the list of command line options to standard output in MediaWiki markup. for when you're being a wiki main character ✨
  • --man — writes the man page source in 'nroff' markup to standard output. meta? we're doing meta 🌀
  • --version — writes the toolkit version to standard output. 🦋
  • --echo — writes the current command line to standard output. so you can see what you just did, no cap 💀
  • --verbose-level <integer> — sets the verbosity level. more number = more talking 🗣️
  • --verbose, -v — increments the verbosity level by 1. deprecated, bestie, but supported for backward compatibility 🫶 (yes we're still keeping it around, don't come for her)
  • --threads <integer> — sets the maximum number of parallel threads (this is for POSIX threads and OpenMP, she's versatile 💪)

👑 Main Options 👑

  • --mask, -m — use reference image pixels as a binary mask. masking era 🎭
  • --target-image-fsl <string> — path to an optional target image to be used in FSL. this is the image that the transformation — and therefore the deformation field it creates — maps to. so here's the thing: when you're making a deformation field for FSL's "applywarp" tool, it may be necessary to determine whether the x coordinate of the resulting deformation vectors has to be flipped. [Default: disabled] 🙈
  • --inversion-tolerance-factor <double> — factor for the numerical tolerance of B-spline inversion [multiples of minimum grid pixel size; default=0.1] [Default: 0.1]. precision queen 👑
  • --downsample <string> — downsample the grid by factors 'x,y,z' or by a single factor 'xyz' [Default: NONE]. choose your reduction, it's giving options ✨
  • --output-absolute — make the output deformation field with absolute target location vectors, rather than relative offset vectors. absolute vs relative, the eternal question 💅

🫶 AUTHORS 🫶

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. a whole squad, we stan a collaborative effort 🌈

📜 LICENSE 📜

http://www.fsf.org/licensing/licenses/gpl.html — GPL, obviously 💖

💀 BUGS 💀

report bugs at http://nitrc.org/projects/cmtk/. not me manifesting zero bugs but okay 🙈

⭐ 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. and from April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381. funding slay 💸✨

and that's the whole page bestie!! this manual is from CMTK 3.3.1p2, dated Jun 24 2026 — genuinely iconic of them to future-date it, we love a time traveler 👑💜 go forth and convert those transformations fr fr 🦋

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