groupwise_warp(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 groupwise_warp(1) 💖

okay bestie, buckle up, this is groupwise_warp from the CMTK (The Computational Morphology Toolkit) crew — a whole entire vibe of a registration tool, and yes, it's from section 1 of the manual, so it's a command you actually run. 🫶

✨ NAME ✨

groupwise_warp — Nonrigid population registration. that's it, that's the whole elevator pitch. 💅

🎀 SYNOPSIS 🎀

groupwise_warp [options] affineGroupRegistration

🌸 DESCRIPTION 🌸

so like, this tool nonrigidly registers a whole population of input images at the same time, no template needed, no cap. it does it one of two ways, and you get to pick:

  • using the 'congealing' algorithm, or
  • using a groupwise similarity measure based on a continuous approximation of mutual information, aka 'RMI'.

that's the tea. it's giving "everybody gets aligned together, main character energy for the entire squad". ✨

👑 OPTIONS 👑

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

like, every CMTK tool has these, they're the group chat everyone's in:

  • --help — writes the list of basic command line options to standard output. baby's first flag. 🍼
  • --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 being wiki-famous. 📝
  • --man — writes man page source in 'nroff' markup to standard output. so meta, we're literally inside this. 😭
  • --version — writes toolkit version to standard output.
  • --echo — writes the current command line to standard output. it's giving receipts. 🧾
  • --verbose-level <integer> — set verbosity level. how much it yaps.
  • --verbose, -v — increment verbosity level by 1 (deprecated; supported for backward compatibility). yes queen, still works, just old. 🙈
  • --threads <integer> — set maximum number of parallel threads (for POSIX threads and OpenMP). multitasking icon. ⚡

💫 Registration Metric Options

pick your fighter, bestie:

  • --rmi — use the RMI (a.k.a. regional mutual information) metric to drive the registration). (yes the paren situation is a little unhinged, we keep it exactly how it is) 💖
  • --congeal — use the congealing algorithm using pixelwise stack entropies to drive the registration. [This is the default] ← so if you say nothing, this is what you get, no questions asked.

💫 Template Image Options

  • --template <string>, -t <string> — override template image with given file. [Default: NONE]
  • --template-with-data <string>, -T <string> — use user-supplied template image's pixel data in registration. [Default: disabled] — note it's off by default, so don't be surprised when it doesn't do the thing.

💫 Multuresolution Parameters

(yes the heading says "Multuresolution", that's canon, I don't make the rules, I just report them) 🌈

  • --downsample-from <integer>, -d <integer> — Initial downsampling factor [4]. [Default: 4]
  • --downsample-to <integer>, -D <integer> — Final downsampling factor [1]. [Default: 1]
  • --sampling-density <float>, -s <float> — Probabilistic sampling density [default: off]. [Default: -1]

💫 Output Options

  • --output-root <string>, -O <string> — Root directory for all output files. [Default: NONE]
  • --output <string>, -o <string> — Output filename for groupwise registration archive. [Default: groupwise.xforms]
  • --output-average <string> — Output filename for registered average image. [Default: average.nii]
  • --no-output-average — Do not write average image. sometimes you just don't want the average, and that's valid. 🙅
  • --average-cubic — Use cubic interpolation for average image (default: linear). fancy smoothing unlocked. ✨

💫 Image Options and Operations

  • --force-background <integer>, -B <integer> — Force background pixels (outside FOV) to given (bin) value. [Default: disabled]
  • --histogram-bins <integer>, -H <integer> — Set number of histogram bins for entropy evaluation. [Default: disabled]
  • --crop-histograms — Crop image histograms to make better use of histogram bins. waste not, want not. 🍓
  • --match-histograms — Match all image histograms to template data (or first image, if no template image is given). (no period, we don't gatekeep punctuation)
  • --repeat-match-histograms — Frequetly repeat histogram-based intensity matching to account for changing volume proportions. (yes, "Frequetly". verbatim. iconic typo behavior, we stan.) 🎀
  • --smooth-pixels <double> — Sigma of Gaussian smoothing kernel in multiples of template image pixel size. [Default: disabled]
  • --smooth-cps <double> — Sigma of Gaussian smoothing kernel in multiples of control point delta. [Default: disabled]

💫 Transformation Parameters

  • --grid-spacing <double> — Control point grid spacing. [Default: 40]
  • --grid-spacing-fit — Use grid spacing that fits volume FOV. ✨ tailored, bespoke, custom.
  • --refine-grid <integer>, -r <integer> — Number of times to refine transformation grid [default: 0]. [Default: 0]

💫 Transformation Constraint Options

  • --zero-sum, -z — Enforce zero-sum computation.
  • --zero-sum-no-affine — Enforce zero-sum computation EXCLUDING affine components. lowercase bestie is not invited here.
  • --normal-group-first-n <integer>, -N <integer> — First N images are from the normal group and should be registered unbiased. [Default: 0]
  • --zero-sum-first-n <integer>, -Z <integer> — Enforce zero-sum computation for first N images. [Default: disabled]
  • --jacobian-weight <float>, -J <float> — Weight for Jacobian volume preservation constraint [default: off]. [Default: 0]
  • --bending-energy-weight <float>, -E <float> — Weight for grid bending energy regularization constraint [default: off]. [Default: 0]

💫 Optimization Parameters

  • --exploration <double>, -e <double> — Exploration of optimization in pixels. [Default: 0.25]
  • --accuracy <double>, -a <double> — Accuracy of optimization in pixels. [Default: 0.01]
  • --step-factor <double>, -S <double> — Step factor for successive optimization passes. [Default: 0.5]
  • --delta-f-threshold <double> — Optional threshold to terminate optimization (level) if relative change of target function drops below this value. [Default: 0]
  • --partial-gradient-thresh <float>, -p <float> — Threshold factor for partial gradient zeroing [<0 turn off]. [Default: 0] — heads up: below zero turns it off, that's the escape hatch.
  • --activate-uninformative — Activate potentially uninformative control points. let them speak, honestly. 🗣️
  • --disable-cp-mask <string> — Path to mask image (matching template grid) defining areas in which control points should be disabled. This guarantees that mask foreground areas remain undeformed. [Default: NONE] — so if you want certain areas to stay exactly as they are, this is your girl.
  • --disable-optimization — Disable optimization and output initial configuration. the "I'm just here to observe" mode. 👀

🫶 AUTHORS 🫶

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

📜 LICENSE 📜

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

😭 BUGS 😭

Report bugs at http://nitrc.org/projects/cmtk/ — they're not gonna fix themselves bestie, speak up!

🌟 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 was CMTK 3.3.1p2, dated Jun 24 2026, and honestly? iconic. slay. periodt. 💅✨🎀🦋

📦 where this page comes from