registration(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 registration(1) 💖

okay bestie, listen UP — this is the registration page from the The Computational Morphology Toolkit (CMTK), and I'm gonna walk you through every single flag like we're sitting in a coffee shop and I'm explaining why this tool is literally the main character of image alignment. ✨

🌸 NAME 🌸

registration — rigid and affine registration 🦋

🎀 SYNOPSIS 🎀

registration ReferenceImage FloatingImage

💫 DESCRIPTION 💫

So what does this do? It performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures. That's the whole vibe. Two images walk in, one transformation walks out. Slay. 💅

✨ OPTIONS ✨

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

Like, these are the communal snacks. Every CMTK tool gets them. 🍓

  • --help — Writes a 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.
  • --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.
  • --xml — Writes the command line syntax specification in XML markup (this one's for Slicer integration).
  • --version — Writes toolkit version to standard output.
  • --echo — Writes 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 — so it's giving "still here, still cute")
  • --threads <integer> — Set maximum number of parallel threads (for POSIX threads and OpenMP).

🤖 Automation Options

  • --auto-multi-levels <integer> — Automatic optimization and resolution parameter generation for <n> levels [Default: 0]

🔥 Optimization settings

  • --exploration <double>, -e <double> — Exploration [that's the initial optimizer step size] [Default: 8]
  • --accuracy <double>, -a <double> — Accuracy [the final optimizer step size] [Default: 0.1]
  • --stepfactor <double>, -f <double> — Factor for search step size reduction. Must be > 0.0 and < 1.0 [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]

🌈 Image resolution parameters

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

💅 Transformation parameters

  • --dofs <integer>[,<integer>,...] — Add number of degrees of freedom [can be repeated]
  • --dofs-final <integer>[,<integer>,...] — Add number of degrees of freedom for the final level only [can be repeated]
  • --no-switch, -n — Do not auto-switch reference and floating image for improved computational performance
  • --initxlate, -i — Initialized transformation by translating floating image FOV center onto reference image FOV center
  • --initial <transformation-path> — Initialize transformation from the given path [Default: NONE]
  • --initial-is-inverse — Invert the initial transformation before initializing registration

🎀 Image data

  • --registration-metric — Registration metric for motion estimation by image-to-image registration. Supported values are "nmi", "mi", "cr", "msd", "ncc", where the default is "nmi" — or just 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.

🧚 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
  • --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

Same energy, other image. 💖

  • --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 the final transformation [Default: NONE]
  • --out-matrix <string> — Output path for the final transformation in matrix format [Default: NONE]
  • --out-parameters <string> — Output path for the final transformation in plain parameter list format [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]

🦋 Import Results into Slicer

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

🗄️ 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 💖

📜 LICENSE 📜

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

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/ — pls do it, they wanna hear from you 🫶

⭐ 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.

aaaand that's the whole thing bestie, you ate that 🎀 no cap, this is CMTK 3.3.1p2, dated Jun 24 2026 — go register some images and be iconic. periodt. 💅✨🦋

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