Provided by: cmtk_3.2.2-1.4_amd64 
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
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.