groupwise_affine(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

✨ NAME ✨

groupwise_affine — affine population registration. That's it, that's the whole girlboss job description. It's page groupwise_affine(1) from the Computational Morphology Toolkit, and she's here to get your whole image squad aligned at the same time. No template needed. Periodt. 💅

🦋 SYNOPSIS 🦋

groupwise_affine [options] image0 [image1 ...]

💖 DESCRIPTION 💖

Okay so here's the tea, bestie ☕ — this tool registers a whole population of input images simultaneously. All at once. Together. No template, no middleman, no "everyone line up behind image zero" energy. It's giving main character ensemble cast. 👑

And how does it do that? You've got two options, lowkey iconic both of them:

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

Choose your fighter, we'll get to the flags below. ✨

🌸 OPTIONS 🌸

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

Like, every CMTK tool has these. They're the family heirlooms. 🫶

  • --help — writes the list of basic command line options to standard output.
  • --help-all — writes the complete list of basic and advanced command line options to standard output. The deluxe edition. 💖
  • --wiki — writes the list of command line options to standard output in MediaWiki markup.
  • --man — writes man page source in 'nroff' markup to standard output.
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output. So you can screenshot it for the group chat, obviously.
  • --verbose-level <integer> — set the verbosity level. Pick your volume. 🔊
  • --verbose, -v — increments verbosity level by 1. It is deprecated; it's supported for backward compatibility only (we keep it around like that one situationship, iykyk).
  • --threads <integer> — set the maximum number of parallel threads (for POSIX threads and OpenMP). Multitasking queen. 👑

🔥 Registration Metric Options

Which metric drives the whole thing.

  • --rmi — use the RMI (a.k.a. regional mutual information) metric to drive the registration.
  • --congeal — use the congealing algorithm, using pixelwise stack entropies to drive the registration. This is the default. The moment. 💅

🎀 Template Image Options

  • --template <string>, -t <string> — input filename for a pre-defined template image. [Default: NONE]
  • --template-with-data <string>, -T <string> — use the user-supplied template image's pixel data in registration. [Default: disabled]

🫶 Output Options

Where all the goods get written, bestie.

  • --output-root <string>, -O <string> — root directory for all output files. [Default: NONE]
  • --output <string>, -o <string> — output filename for the groupwise registration archive. [Default: groupwise.xforms]
  • --output-average <string> — output filename for the registered average image. [Default: average.nii]
  • --average-linear — use linear interpolation for the average image. This is the default.
  • --average-cubic — use cubic interpolation for the average image. Fancier, slower, ✨vibes✨.
  • --no-output-average — do not write the average image. Sometimes you just don't want the souvenir.

🌈 Multiresolution Parameters

  • --downsample-from <integer>, -d <integer> — initial downsampling factor. [Default: 4]
  • --downsample-to <integer>, -D <integer> — final downsampling factor. [Default: 1]
  • --sampling-density <float>, -s <float> — probabilistic sampling density. Legal values are between 0 and 1. [Default: disabled]

🦋 Image Options and Operations

  • --force-background <integer>, -B <integer> — force background pixels (outside FOV) to the given (bin) value. [Default: disabled]
  • --histogram-bins <integer>, -H <integer> — manually set the number of histogram bins for entropy evaluation. [Default: disabled]
  • --crop-histograms — crop image histograms to make better use of the histogram bins.
  • --smooth <double> — sigma of the Gaussian smoothing kernel, in multiples of the template image pixel size. [Default: disabled]
  • --match-histograms — match all image histograms to the template data (or to the first image, if no template image is given).
  • --free-and-reread — free memory allocated for the original images whenever they're not needed, and re-read the image files as needed. This can be useful when running on a machine with limited memory resources. Very "my laptop is fighting for its life" core. 😭

👑 Transformation Parameters

  • --dofs <integer>[,<integer>,...] — add DOFs to the list. [Default: one pass, 6 DOF]
  • --zero-sum, -z — enforce zero-sum computation.
  • --normal-group-first-n <integer>, -N <integer> — the 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 the first N images. [Default: disabled]

⭐ Transformation Initialization

  • --align-bounding-boxes — initially align the centers of the bounding boxes of all images by translations. This is the default.
  • --align-centers-of-mass — initially align the centers of mass by translations.
  • --init-scales — initialize the scale factors using first-order moments.

💜 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]
  • --repeat-level <integer>, -r <integer> — number of repetitions per optimization level. [Default: 5]
  • --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 the relative change of the target function drops below this value. [Default: 0]
  • --disable-optimization — disable optimization and output the initial configuration. Do not pass go, do not collect your optimized transform. 🚫

🫶 AUTHORS 🫶

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. The whole crew ate and left no crumbs. 👑

📜 LICENSE 📜

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

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/ — tell them everything, babes, they want the details.

🌟 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. Institutional support? We love to see it. 💖

And that's the page, bestie — this is CMTK version 3.3.1p2, dated Jun 24 2026. Go register your population, slay, and don't forget to cite. Mwah. 💅✨

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