mcwarp

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)

--help: Write list of basic command line options to standard output.
--help-all: Write complete list of basic and advanced command line options to standard output.
--wiki: Write list of command line options to standard output in MediaWiki markup.
--man: Write man page source in 'nroff' markup to standard output.
--version: Write toolkit version to standard output.
--echo: Write 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).
--threads <integer>: Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

--out-archive <string>, -o <string>: Output archive path. [Default: NONE]
--downsample-from <integer>, -d <integer>: Initial downsampling factor [1]. [Default: 1]
--downsample-to <integer>, -D <integer>: Final downsampling factor [1]. [Default: 1]
--downsample-average <boolean>: Downsample using sliding-window averaging [default: off] ) [Default: 0]
--smooth <float>: Sigma of Gaussian smoothing kernel in multiples of template image pixel size [default: off] ) [Default: 0]
--grid-spacing <double>: Initial control point grid spacing in mm. [Default: 40]
--grid-spacing-exact <double>: Exact initial grid spacing, even if it doesn't match image FOV. [Default: disabled]
--refine-grid <integer>: Number of control point grid refinements. [Default: 0]
--delay-refine-grid: Delay control point grid refinement until after pixel refinement.
--adaptive-fix-thresh-factor <float>: Intensity threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: 0]
--adaptive-fix-thresh-factor-entropy <float>: Entropy threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing] [Default: disabled]
--fix-warp-x: Fix transformation (do not warp) in x-direction.
--fix-warp-y: Fix transformation (do not warp) in y-direction.
--fix-warp-z: Fix transformation (do not warp) in z-direction.
--jacobian-constraint-weight <float>: Weight for Jacobian volume preservation constraint [Default: 0]
--histograms, -H: Use multi-dimensional histograms to compute entropies [default. [This is the default]
--covariance, -C: Use covariance matrix determinants to compute entropies.
--cubic, -c: Use cubic interpolation [default: linear]
--mi: Use standard mutual information metric [default] [This is the default]
--nmi: Use normalized mutual information metric
--intensity-correction, -I: Correct image intensities using local transformation Jacobian to preserve total signal
--initial-step-size <double>: Initial optimizer step size in pixels. [Default: 1]
--final-step-size <double>: Initial optimizer step size in pixels. [Default: 0.125]
--delta-f-threshold <double>: 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/

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.

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