jidb(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 jidb — bestie edition 💖

okay so you've found yourself on the jidb(1) page, which lives in The Computational Morphology Toolkit (yes, that CMTK, the one we're all obsessed with). pull up a chair, grab a strawberry 🍓, and let's get into it.

✨ NAME ✨

jidb — fixes interleaved motion using joint iterative deblurring. that's the whole job. that's the assignment. and it ate. 💅

🦋 SYNOPSIS 🦋

jidb [options] inImage outImage

🌸 DESCRIPTION 🌸

so what this tool literally does is: it takes your interleaved input image, splits it into the pass images (all of them, one by one, no crumbs left), co-registers them with each other, and then reconstructs a motion-corrected image. iconic behavior. no cap. ✨

👑 OPTIONS 👑

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

these are the group-chat-everyone-is-in options. every CMTK tool has them, so you already kinda know them:

  • --help — writes the list of basic command line options to standard output. your starter pack 🫶
  • --help-all — writes the complete list of both 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 need it wiki-fied.
  • --man — writes man page source in 'nroff' markup to standard output. yes, it generates the very thing you're reading. meta king behavior 👑
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output.
  • --verbose-level <integer> — sets the verbosity level. you control the yapping.
  • --verbose, -v — increments the verbosity level by 1. deprecated — it's only still here for backward compatibility, so like, it works but it's giving legacy 🙈
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). multitasking queen.

🧚 Interleaving Options

  • --interleave-axis — defines the interleave axis: this is the through-slice direction of the acquisition. supported values: "guess-from-input", "axial", "sagittal", "coronal", "interleave-x", "interleave-y", "interleave-z", where the default is "guess-from-input". or, alternatively, just use one of these cuties right here:
    • --guess-from-input — guess from input image [This is the default]
    • --axial, -a — interleaved axial images
    • --sagittal, -s — interleaved sagittal images
    • --coronal, -c — interleaved coronal images
    • --interleave-x, -x — interleaved along x axis
    • --interleave-y, -y — interleaved along y axis
    • --interleave-z, -z — interleaved along z axis
  • --passes <integer>, -p <integer> — number of interleaved passes [Default: 2]
  • --pass-weight <string>, -W <string> — sets the contribution weight for a pass, in the form 'pass:weight'

🔥 Motion Correction / Registration Options

  • --reference-image <image-path>, -R <image-path> — use a separate high-resolution reference image for registration [Default: NONE]
  • --registration-metric — the registration metric used for motion estimation by image-to-image registration. supported values: "nmi", "mi", "cr", "msd", "cc", where the default is "msd", or use one of the following:
    • --nmi — use Normalized Mutual Information for pass-to-refereence registration
    • --mi — use standard Mutual Information for pass-to-refereence registration
    • --cr — use Correlation Ratio for pass-to-refereence registration
    • --msd — use Mean Squared Differences for pass-to-refereence registration [This is the default]
    • --cc — use Cross-Correlation for pass-to-refereence registration
  • --import-xforms-path <path> — path of file from which to import transformations between passes. [Default: NONE]
  • --export-xforms-path <path> — path of file to which to export transformations between passes. [Default: NONE]

🎀 Volume Injection Options

  • --injection-kernel-sigma <double>, -S <double> — standard deviation of Gaussian kernel for volume injection [Default: 1]
  • --injection-kernel-radius <integer>, -r <integer> — truncation radius of injection kernel [Default: 4]

💜 Deblurring Options

  • --psf — kernel for the inverse interpolation reconstruction. supported values: "box", "gaussian", or use one of the following:
    • --box — box-shaped PSF
    • --gaussian — Gaussian-shaped PSF
  • --psf-scale <double> — sets the global scale factor for the point spread function size, which itself is derived from the input image. [Default: 1]

⭐ Optimization Options

  • --fourth-order-error, -f — use fourth-order error (rather than second-order) for optimization.
  • --num-iterations <integer>, -n <integer> — maximum number of inverse interpolation iterations [Default: 20]
  • --no-truncation, -T — turn off regional intensity truncatrion 🙈
  • --l-norm-weight <double> — set constraint weight for Tikhonov-type L-Norm regularization (0 disables the constraint) [Default: 0]

🩷 Output Options

  • --write-injected-image <image-path> — write initial volume injection image to path [Default: NONE]
  • --write-images-as-float, -F — write 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. a whole squad, fr fr 🫶

📜 LICENSE 📜

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

💀 BUGS 💀

found a bug? report it at http://nitrc.org/projects/cmtk/ — they wanna hear it, bestie.

🌟 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. shoutout to the funders, they understood the vision 💖

and that's the whole page, gorgeous. this is CMTK 3.3.1p2, dated Jun 24 2026 — jot that down, screenshot it, put it in the group chat, because you're now officially fluent in jidb(1). slay, go fix that interleaved motion 🦋✨💅

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