warp(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ warp(1) — the B-spline nonrigid registration bestie ✨

Okay so like, welcome to warp, part of The Computational Morphometry Toolkit (CMTK, for the girlies in the know 💅). It does B-spline nonrigid registration and honestly? It ate.

🌸 NAME 🌸

warp — B-spline nonrigid registration. That's it, that's the vibe.

🦋 SYNOPSIS 🦋

warp ReferenceImage FloatingImage InitialXform

Three little args, one big glow-up for your images ✨

💖 DESCRIPTION 💖

So basically, this program performs nonrigid image registration using multi-resolution optimization of voxel-based image similarity measures and a multi-resolution B-spline transformation model.

Translation for the besties: it wiggles your image around in a bendy, squishy, spline-y way until it lines up with another image, and it does it at multiple zoom levels like a queen who checks her makeup from far away and up close. 🪞👑

👑 OPTIONS 👑

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

These ones are the communal closet — every CMTK tool gets to borrow them, no cap.

  • --help — Writes the list of basic command line options to standard output. The "just tell me the basics" button.
  • --help-all — Writes the complete list of basic and advanced command line options to standard output. The "give me everything, I can handle it" button 🔥
  • --wiki — Writes the list of command line options to standard output in MediaWiki markup. For when your docs live on a wiki, periodt.
  • --man — Writes man page source in nroff markup to standard output. Meta, iconic, no notes.
  • --xml — Writes the command line syntax specification in XML markup (for Slicer integration). Slicer girlies, this one's for you 🫶
  • --version — Writes the toolkit version to standard output. Vibe check the release.
  • --echo — Writes the current command line to standard output. It's giving receipts.
  • --verbose-level <integer> — Sets the verbosity level. Turn the yapping up or down.
  • --verbose, -v — Increments the verbosity level by 1. Heads up bestie: this is deprecated, it's only supported for backward compatibility. 💀
  • --threads <integer> — Sets the maximum number of parallel threads (for POSIX threads and OpenMP). More threads, more speed, more main character energy.

🧚 Transformation import/export

  • --initial <transformation-path> — Initialize transformation from given path [Default: NONE]
  • --write-itk-xform <transformation-path> — Output path for the final transformation in ITK format [Default: NONE]
  • --write-reformatted <image-path> — Write the reformatted floating image. [Default: NONE]

🌸 Transformation parameters

  • --grid-spacing <double>, -g <double> — Control point grid spacing [Default: 15]
  • --exact-spacing — Use exact control point spacing; do not modify spacing to fit the reference image bounding box. No fitting, no compromising. 💅
  • --refine <integer> — Number of refinements (control point grid resolution levels) [Default: 0]
  • --delay-refine — Delay control point grid refinement; first switch to the next higher image resolution.
  • --ignore-edge <integer> — Ignore n control point layers along each image face [Default: 0]
  • --restrict <string> — Restrict deformation to coordinate dimension(s) [one or more of 'x','y','z'] [Default: NONE]
  • --no-adaptive-fix — Disable adaptive fixing of control points; optimize all deformation parameters.
  • --adaptive-fix-thresh <float> — Threshold factor for entropy criterion to fix local control points [Default: 0.5]
  • --accurate — Accurate computation mode: may give slightly better results after substantially longer computation. [This is the default]
  • --fast — Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time. 🏃‍♀️💨
  • --switch, -S — Switch reference and floating image. Swap era. 🔄

🎀 Regularization parameters

  • --jacobian-weight <float> — Weight for Jacobian-based local volume preservation constraint [Default: 0]
  • --energy-weight <float> — Weight for grid bending energy constraint [Default: 0]
  • --rigidity-weight <float> — Weight for local rigidity constraint [Default: 0]
  • --ic-weight <float> — Weight for inverse consistency constraint [Default: 0]
  • --relax <float> — Weight relaxation factor for alternating under-constrained iterations [Default: -1]
  • --relax-to-unfold — Before each resolution level, regularize negative-Jacobian areas of the deformation to unfold them. Unfolding the chaos, one layer at a time 🫶

⭐ Optimization parameters

  • --exploration <double>, -e <double> — Search space exploration (initial step size) [Default: -1]
  • --accuracy <double>, -a <double> — Search accuracy (initial step size) [Default: -1]
  • --stepfactor <double>, -f <double> — Factor for search step size reduction. Must be > 0.0 and < 1.0 [default: 0.5] [Default: 0.5]
  • --delta-f-threshold <double> — Optional threshold to terminate optimization (level) if the relative change of target function drops below this value. [Default: 0]
  • --no-maxnorm — Use the Euclid norm for gradient normalication in optimization, rather than the maximum norm. (Yes, "normalication" — we're quoting the original, don't come for us 😭)

💜 Image resolution parameters

  • --sampling <double>, -s <double> — Image sampling (finest resampled image resolution) [Default: -1]
  • --coarsest <double> — Upper limit for image sampling in multiresolution hierarchy [Default: -1]
  • --omit-original-data — Do not use original data in full resolution for the final registration stage.

🌈 Image data

  • --registration-metric — Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "msd", "ncc", where the default is "nmi", or use one of the following:
    • --nmi — Normalized Mutual Information metric [This is the default]
    • --mi — Standard Mutual Information metric
    • --cr — Correlation Ratio metric
    • --msd — Mean Squared Difference metric
    • --ncc — Normalized Cross Correlation metric
  • --match-histograms — Match floating image histogram to reference image histogram. Twin energy ✨
  • --force-outside-value <double> — Force values outside the field of view to this value rather than drop incomplete pixel pairs [Default: disabled]

🍓 Reference Image Preprocessing

  • --class-ref <string> — Data class: grey (default) or label [Default: NONE]
  • --pad-ref <double> — Padding value [Default: disabled]
  • --thresh-min-ref <double> — Minimum value truncation threshold [Default: disabled]
  • --thresh-max-ref <double> — Maximum value truncation threshold [Default: disabled]
  • --prune-histogram-ref <integer> — Number of bins for histogram-based pruning [Default: disabled]
  • --histogram-equalization-ref — Apply histogram equalization
  • --sobel-filter-ref — Apply Sobel edge detection filter. Edge. Literally. 🔪
  • --crop-index-ref <string> — Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
  • --crop-world-ref <string> — Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]

🦋 Floating Image Preprocessing

  • --class-flt <string> — Data class: grey (default) or label [Default: NONE]
  • --pad-flt <double> — Padding value [Default: disabled]
  • --thresh-min-flt <double> — Minimum value truncation threshold [Default: disabled]
  • --thresh-max-flt <double> — Maximum value truncation threshold [Default: disabled]
  • --prune-histogram-flt <integer> — Number of bins for histogram-based pruning [Default: disabled]
  • --histogram-equalization-flt — Apply histogram equalization
  • --sobel-filter-flt — Apply Sobel edge detection filter
  • --crop-index-flt <string> — Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
  • --crop-world-flt <string> — Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]

🌟 Output parameters

  • --outlist <string>, -o <string> — Output path for final transformation [Default: NONE]
  • --protocol <string>, -p <string> — Optimization protocol output file name [Default: NONE]
  • --time <string>, -t <string> — Computation time statistics output file name [Default: NONE]
  • --output-intermediate — Write transformation for each level [default: only write final transformation]

🧚 Image/Transformation Database

  • --db <string> — Path to image/transformation database that should be updated with the new registration and/or reformatted image. [Default: NONE]

💫 AUTHORS 💫

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. Legends, all of them 👑👑

📜 LICENSE 📜

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

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/. Not me manifesting a bug-free run 🙈 but if it happens, tell the devs, not the group chat.

🫶 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.

And that's the whole page, bestie 💖 This one's from CMTK 3.3.1p2, dated Jun 24 2026 — so like, shoutout to the version and the date, they're both serving. Go register something nonrigidly. Slay. ✨💅🦋

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