TEND-FIBER(1)

✨ TEND-FIBER(1) ✨ — it's giving fiber tractography

okay so bestie, welcome to tend-fiber, a User Commands moment, and honestly? she's a whole icon. let's get into it 💅

🎀 NAME 🎀

tend-fiber — fiber tractography, from one or more seeds

🦋 SYNOPSIS 🦋

tend fiber [-i <nin>] [-dwi] [-s <seed point>] [-ns <seed nrrd>] [-wsp]
[-t <type>] [-n <intg>] [-k <kernel>] [-wp <which>] [-ap] [-wspo] [-step
<step size>] -stop <stop1 ...> [-v <verbose>] [-nmat <transform>] [-o
<nout>]

🌸 DESCRIPTION 🌸

So like, tend-fiber does fiber tractography, from one or more seeds. Periodt.

She's a fairly complete command-line interface to the tenFiber API — like, the whole vibe is right there on your terminal, no cap. 🫶

💖 OPTIONS 💖

• -i <nin> — the input volume, bestie. default: "-"
• -dwi — tells her the input volume is a DWI volume and NOT a single tensor volume. very much a different situation, okay? 🔥
• -s <seed point> — the seed point for the fiber; she will propogate in two opposite directions starting from here, and yes that's 3 doubles. default: "0 0 0" ✨
• -ns <seed nrrd> — a 3-by-N nrrd of seedpoints. default: ""
• -wsp — define seedpoint and output path in worldspace. Otherwise — like, if you don't use this option — everything is in index space. iykyk
• -t <type> — fiber type. defaults to something (it's a string, she's mysterious like that) 🙈
• -n <intg> — the integration method for fiber tracking. default: "rk4"
• -k <kernel> — the kernel for reconstructing the tensor field. default: "tent"
• -wp <which> — when you're doing multi-tensor tracking, this is the index of the path to follow (and it gets made moot by -ap, so). it's an unsigned int. default: "0"
• -ap — follow all paths from (all) seedpoint(s)!! and the output will be polydata rather than a single 3-by-N nrrd — even if only a single path is generated. slay
• -wspo — output should be in worldspace, even if input is not. > this feature is unstable and/or confusing 💀 so like, tread carefully bestie
• -s <step size> — stepsize along fiber, in world space. it's a double. default: "0.01" (yes, -s shows up twice in this manpage, and yes, we're just going to respect that, no questions asked 🎀)
• -stop <stop1 ...> — the conditions that should signify the end of a fiber, or when to discard a fiber that is done propagating. multiple stopping criteria are logically OR-ed and tested at every point along the fiber. the possibilities include:
  • "aniso:<type>,<thresh>": require anisotropy to be above the given threshold. which anisotropy type you ask? given as with tend-anvol(1) 🦋
  • "len:<length>": limits the length, in world space, of each fiber half
  • "steps:<N>": the number of steps in each fiber half is capped at N
  • "conf:<thresh>": requires the tensor confidence value to be above the given thresh
  • "radius:<thresh>": requires that the radius of curvature of the fiber stay above given thresh
  • "frac:<F>": in multi-tensor tracking, the fraction of the tracked component must stay above F
  • "minlen:<len>": discard fiber if its final whole length is below len (not really a termination criterion, she's just like that)
  • "minsteps:<N>": discard fiber if its final number of steps is below N (also not really a termination criterion) — and you need 1 or more fiber stops, so don't skip this one 💅
• -v <verbose> — verbosity level, an int. default: "0"
• -nmat <transform> — a 4x4 homogenous transform matrix (given as a nrrd, or honestly just a text file) passed with this option will be applied to the output tractography vertices just prior to output. default: "" ✨
• -o <nout> — output fiber(s), a string. default: "-"

👑 SEE ALSO 👑

tend(1), tend-anvol(1)

and that's the whole page, bestie 🫶 this was TEND-FIBER(1), from the User Commands corner of the manual, dated April 2021 — she's an older queen but she still ate. go track some fibers, ily, bye 💖✨🌈