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mcwarp(1) The Computational Morphometry Toolkit mcwarp(1)

NAME

mcwarp - Multi-channel nonrigid registration

SYNOPSIS

mcwarp [options] mcaffineOutput

DESCRIPTION

Multi-channel nonrigid B-spline image registration using histogram-based or covariance-based joint entropy 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 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).

Main Options

Output archive path. [Default: NONE]
Initial downsampling factor [1]. [Default: 1]
Final downsampling factor [1]. [Default: 1]
Downsample using sliding-window averaging [default: off] ) [Default: 0]
Sigma of Gaussian smoothing kernel in multiples of template image pixel size [default: off] ) [Default: 0]
Initial control point grid spacing in mm. [Default: 40]
Exact initial grid spacing, even if it doesn't match image FOV. [Default: disabled]
Number of control point grid refinements. [Default: 0]
Delay control point grid refinement until after pixel refinement.
Intensity threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: 0]
Entropy threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: disabled]
Fix transformation (do not warp) in x-direction.
Fix transformation (do not warp) in y-direction.
Fix transformation (do not warp) in z-direction.
Weight for Jacobian volume preservation constraint [Default: 0]
Use multi-dimensional histograms to compute entropies [default. [This is the default]
Use covariance matrix determinants to compute entropies.
Use cubic interpolation [default: linear]
Use standard mutual information metric [default] [This is the default]
Use normalized mutual information metric
Correct image intensities using local transformation Jacobian to preserve total signal
Initial optimizer step size in pixels. [Default: 1]
Initial optimizer step size in pixels. [Default: 0.125]
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

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.

Jun 6 2022 CMTK 3.3.1p2