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registration(1) The Computational Morphometry Toolkit registration(1)

NAME

registration - Rigid and affine registration

SYNOPSIS

registration ReferenceImage FloatingImage

DESCRIPTION

This program performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures.

OPTIONS

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

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write command line syntax specification in XML markup (for Slicer integration).
Write toolkit version to standard output.
Write the current command line to standard output.
Set verbosity level.
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Automation Options

Automatic optimization and resolution parameter generation for <n> levels [Default: 0]

Optimization settings

Exploration [initial optimizer step size] [Default: 8]
Accuracy [final optimizer step size] [Default: 0.1]
Factor for search step size reduction. Must be > 0.0 and < 1.0 [Default: 0.5]
Optional threshold to terminate optimization (level) if relative change of target function drops below this value. [Default: 0]

Image resolution parameters

Image sampling (finest resampled image resolution) [Default: 1]
Upper limit for image sampling in multiresolution hierarchy [Default: -1]
Do not use original data in full resolution, omit final stage in multiresolution hierarchy, thus reducing computation time.

Transformation parameters

Add number of degrees of freedom [can be repeated]
Add number of degrees of freedom for final level only [can be repeated]
Do not auto-switch reference and floating image for improved computational performance
Initialized transformation by translating floating image FOV center onto reference image FOV center
Initialize transformation from given path [Default: NONE]
Invert initial transformation before initializing registration

Image data

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:
Normalized Mutual Information metric [This is the default]
Standard Mutual Information metric
Correlation Ratio metric
Mean Squared Difference metric
Normalized Cross Correlation metric
Match floating image histogram to reference image histogram.

Reference Image Preprocessing

Data class: grey (default) or label [Default: NONE]
Padding value [Default: disabled]
Minimum value truncation threshold [Default: disabled]
Maximum value truncation threshold [Default: disabled]
Number of bins for histogram-based pruning [Default: disabled]
Apply histogram equalization
Apply Sobel edge detection filter
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
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

Data class: grey (default) or label [Default: NONE]
Padding value [Default: disabled]
Minimum value truncation threshold [Default: disabled]
Maximum value truncation threshold [Default: disabled]
Number of bins for histogram-based pruning [Default: disabled]
Apply histogram equalization
Apply Sobel edge detection filter
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]

Output parameters

Output path for final transformation [Default: NONE]
Output path for final transformation in matrix format [Default: NONE]
Output path for final transformation in plain parameter list format [Default: NONE]
Optimization protocol output file name [Default: NONE]
Computation time statistics output file name [Default: NONE]

Import Results into Slicer

Output path for final transformation in ITK format [Default: NONE]
Write reformatted floating image. [Default: NONE]

Image/Transformation Database

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/

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.

Jul 7 2024 CMTK 3.3.1p2