cmtk-mcwarp - Online in the Cloud

PROGRAM:

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)
--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

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