mcwarp(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 mcwarp(1) 💖

okay bestie, welcome to mcwarp(1), a.k.a. The Computational Morphometry Toolkit's own multi-channel nonrigid registration icon ✨ she lives in the CMTK family, and no cap, she's a lot — but we're gonna get through it together 🫶

✨ NAME ✨

mcwarp — Multi-channel nonrigid registration 💅

🎀 SYNOPSIS 🎀

mcwarp [options] mcaffineOutput

like… yes, that's the whole vibe. one required-ish thingy, and a whole buffet of options 🌸

🦋 DESCRIPTION 🦋

Multi-channel nonrigid B-spline image registration using histogram-based or covariance-based joint entropy measures 🔥

that's the actual job, fr fr. she aligns images with B-splines, she does it nonrigidly, and she can juggle multiple channels at once. her measure of "how good is this alignment" is either histograms or covariance — you get to pick, main character energy 👑

💅 OPTIONS 💅

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

these are the group-chat-wide settings, every CMTK tool got them, not just our girl:

  • --help — Write list of basic command line options to standard output.
  • --help-all — Write complete list of basic and advanced command line options to standard output. (the full lore drop 📚)
  • --wiki — Write list of command line options to standard output in MediaWiki markup.
  • --man — Write man page source in 'nroff' markup to standard output.
  • --version — Write toolkit version to standard output.
  • --echo — Write the current command line to standard output.
  • --verbose-level <integer> — Set verbosity level.
  • --verbose, -v — Increment verbosity level by 1 (deprecated; supported for backward compatibility). yep, deprecated, but she's still here for the old heads 🙈
  • --threads <integer> — Set maximum number of parallel threads (for POSIX threads and OpenMP). parallelize her, she eats 💀

👑 Main Options

this is the good part. the actual levers. the real ones.

  • --out-archive <string>, -o <string> — Output archive path. [Default: NONE]
  • --downsample-from <integer>, -d <integer> — Initial downsampling factor [1]. [Default: 1]
  • --downsample-to <integer>, -D <integer> — Final downsampling factor [1]. [Default: 1]
  • --downsample-average <boolean> — Downsample using sliding-window averaging [default: off] ) [Default: 0]
  • --smooth <float> — Sigma of Gaussian smoothing kernel in multiples of template image pixel size [default: off] ) [Default: 0]
  • --grid-spacing <double> — Initial control point grid spacing in mm. [Default: 40]
  • --grid-spacing-exact <double> — Exact initial grid spacing, even if it doesn't match image FOV. [Default: disabled]
  • --refine-grid <integer> — Number of control point grid refinements. [Default: 0]
  • --delay-refine-grid — Delay control point grid refinement until after pixel refinement.
  • --adaptive-fix-thresh-factor <float> — Intensity threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: 0]
  • --adaptive-fix-thresh-factor-entropy <float> — Entropy threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: disabled]
  • --fix-warp-x — Fix transformation (do not warp) in x-direction.
  • --fix-warp-y — Fix transformation (do not warp) in y-direction.
  • --fix-warp-z — Fix transformation (do not warp) in z-direction.
  • --jacobian-constraint-weight <float> — Weight for Jacobian volume preservation constraint [Default: 0]
  • --histograms, -H — Use multi-dimensional histograms to compute entropies [default. [This is the default]
  • --covariance, -C — Use covariance matrix determinants to compute entropies.
  • --cubic, -c — Use cubic interpolation [default: linear]
  • --mi — Use standard mutual information metric [default] [This is the default]
  • --nmi — Use normalized mutual information metric
  • --intensity-correction, -I — Correct image intensities using local transformation Jacobian to preserve total signal
  • --initial-step-size <double> — Initial optimizer step size in pixels. [Default: 1]
  • --final-step-size <double> — Initial optimizer step size in pixels. [Default: 0.125]
  • --delta-f-threshold <double> — Optional threshold to terminate optimization (level) if relative change of target function drops below this value. [Default: 0]

🫶 AUTHORS 🫶

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

the whole squad ate, no crumbs 🌟

💜 LICENSE 💜

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

😭 BUGS 😭

Report bugs at http://nitrc.org/projects/cmtk/

not me making you file a bug report… but if she's acting up, that's the link, 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.

and that's the whole page, periodt 💖 this was CMTK 3.3.1p2, dated Jun 24 2026 — she's giving "still thriving" and we're obsessed 👑✨ go register something, you got this 🦋

📦 where this page comes from