fibxform(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ fibxform(1) — the CMTK glow-up for your fiber points ✨

okay bestie, so this is fibxform, section 1 of the Computational Morphology Toolkit man pages, and it's literally the little tool that takes your .fib fiber points and moves them where they belong. let's get into it 💖

🎀 NAME 🎀

fibxform — apply coordinate transformations to point coordinates in .fib file.

(yes that's the whole name section, she's short and she knows it 💅)

🦋 SYNOPSIS 🦋

fibxform XformList

🌸 DESCRIPTION 🌸

okay so picture this: a file with fiber tracking results from the UNC Fiber Tracking tool comes in on Standard Input. fibxform reads it, then applies one or more coordinate transformations to all the fiber point coordinates — and when we say "one or more," we mean you can just concatenate them, they stack, no cap.

the result gets written back out to Standard Output, and it's still in UNC fiber file format, so nothing downstream is confused. slay ✨

💜 OPTIONS 💜

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

like, the whole toolkit has these, every single tool, so you already know her:

  • --help — writes the list of basic command line options to standard output. your little starter pack 🫶
  • --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're documenting, bestie 📝
  • --man — writes man page source in 'nroff' markup to standard output. meta, honestly.
  • --version — writes the toolkit version to standard output. flex check 🌈
  • --echo — writes the current command line to standard output.
  • --verbose-level <integer> — sets the verbosity level. pick your yap level 💀
  • --verbose, -v — increments the verbosity level by 1. ⚠️ deprecated, but supported for backward compatibility, so she still shows up for her friends.
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). go faster, girlie 🔥

🌟 Main Options

  • --inversion-tolerance <double> — the numerical tolerance of B-spline inversion, measured in mm. smaller values = more accurate inversion, but lowkey they may also increase the failure rate, so it's giving tradeoff. [Default: 0.001]
  • --source-image <image-path> — sets the source image of the transformation (i.e., an image defining the space in which fiber tracking was performed), which corrects for differences in orientation and coordinate space. [Default: NONE]
  • --target-image <image-path> — sets the target image of the transformation (i.e., the image that the fiber track points are mapped into), which corrects for differences in orientation and coordinate space. [Default: NONE]
🚨 reminder bestie: --source-image and --target-image default to NONE, so if you need that orientation/coordinate-space correction, you have to ask for it. she's not gonna read your mind 💅

🙈 AUTHORS 🙈

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

📜 LICENSE 📜

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

💀 BUGS 💀

report bugs at http://nitrc.org/projects/cmtk/ — they want to hear from you, fr fr 🐛

🫶 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. the way that funding carried this whole thing 😭💖

and that's the whole page, bestie! this one's CMTK 3.3.1p2, dated Jun 24 2026, and she ate, no crumbs 🎀✨ mwah 💅

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