.TH mcwarp "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
mcwarp \- Multi-channel nonrigid registration
.SH SYNOPSIS
mcwarp [options] mcaffineOutput
.SH DESCRIPTION
Multi-channel nonrigid B-spline image registration using histogram-based or covariance-based joint entropy measures
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Main Options
.TP 5
\fB\-\-out-archive\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output archive path.
.B [Default: NONE]
.TP 5
\fB\-\-downsample-from\fR \fI<integer>\fR, \fB\-d\fR \fI<integer>\fR
Initial downsampling factor [1].
.B [Default: 1]
.TP 5
\fB\-\-downsample-to\fR \fI<integer>\fR, \fB\-D\fR \fI<integer>\fR
Final downsampling factor [1].
.B [Default: 1]
.TP 5
\fB\-\-downsample-average\fR \fI<boolean>\fR
Downsample using sliding-window averaging [default: off] )
.B [Default: 0]
.TP 5
\fB\-\-smooth\fR \fI<float>\fR
Sigma of Gaussian smoothing kernel in multiples of template image pixel size [default: off] )
.B [Default: 0]
.TP 5
\fB\-\-grid-spacing\fR \fI<double>\fR
Initial control point grid spacing in mm.
.B [Default: 40]
.TP 5
\fB\-\-grid-spacing-exact\fR \fI<double>\fR
Exact initial grid spacing, even if it doesn't match image FOV.
.B [Default: disabled]
.TP 5
\fB\-\-refine-grid\fR \fI<integer>\fR
Number of control point grid refinements.
.B [Default: 0]
.TP 5
\fB\-\-delay-refine-grid\fR
Delay control point grid refinement until after pixel refinement.
.TP 5
\fB\-\-adaptive-fix-thresh-factor\fR \fI<float>\fR
Intensity threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing]
.B [Default: 0]
.TP 5
\fB\-\-adaptive-fix-thresh-factor-entropy\fR \fI<float>\fR
Entropy threshold factor [0..1] for adaptive parameter fixing. [default: 0 -- no fixing]
.B [Default: disabled]
.TP 5
\fB\-\-fix-warp-x\fR
Fix transformation (do not warp) in x-direction.
.TP 5
\fB\-\-fix-warp-y\fR
Fix transformation (do not warp) in y-direction.
.TP 5
\fB\-\-fix-warp-z\fR
Fix transformation (do not warp) in z-direction.
.TP 5
\fB\-\-jacobian-constraint-weight\fR \fI<float>\fR
Weight for Jacobian volume preservation constraint
.B [Default: 0]
.TP 5
\fB\-\-histograms\fR, \fB\-H\fR
Use multi-dimensional histograms to compute entropies [default.
\fB[This is the default]\fR
.TP 5
\fB\-\-covariance\fR, \fB\-C\fR
Use covariance matrix determinants to compute entropies.
.TP 5
\fB\-\-cubic\fR, \fB\-c\fR
Use cubic interpolation [default: linear]
.TP 5
\fB\-\-mi\fR
Use standard mutual information metric [default]
\fB[This is the default]\fR
.TP 5
\fB\-\-nmi\fR
Use normalized mutual information metric
.TP 5
\fB\-\-intensity-correction\fR, \fB\-I\fR
Correct image intensities using local transformation Jacobian to preserve total signal
.TP 5
\fB\-\-initial-step-size\fR \fI<double>\fR
Initial optimizer step size in pixels.
.B [Default: 1]
.TP 5
\fB\-\-final-step-size\fR \fI<double>\fR
Initial optimizer step size in pixels.
.B [Default: 0.125]
.TP 5
\fB\-\-delta-f-threshold\fR \fI<double>\fR
Optional threshold to terminate optimization (level) if relative change of target function drops below this value.
.B [Default: 0]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.