.TH groupwise_warp "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
groupwise_warp \- Nonrigid population registration
.SH SYNOPSIS
groupwise_warp [options] affineGroupRegistration
.SH DESCRIPTION
This tool nonrigidly registers a population of input images simultaneously, without a template, using either the 'congealing' algorithm or a groupwise similarity measure based on a continuous approximation of mutual information ('RMI').
.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 Registration Metric Options
.TP 5
\fB\-\-rmi\fR
Use the RMI (a.k.a. regional mutual information) metric to drive the registration).
.TP 5
\fB\-\-congeal\fR
Use the congealing algorithm using pixelwise stack entropies to drive the registration.
\fB[This is the default]\fR
.SS Template Image Options
.TP 5
\fB\-\-template\fR \fI<string>\fR, \fB\-t\fR \fI<string>\fR
Override template image with given file.
.B [Default: NONE]
.TP 5
\fB\-\-template-with-data\fR \fI<string>\fR, \fB\-T\fR \fI<string>\fR
Use user-supplied template images's pixel data in registration
.B [Default: disabled]
.SS Multuresolution Parameters
.TP 5
\fB\-\-downsample-from\fR \fI<integer>\fR, \fB\-d\fR \fI<integer>\fR
Initial downsampling factor [4].
.B [Default: 4]
.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\-\-sampling-density\fR \fI<float>\fR, \fB\-s\fR \fI<float>\fR
Probabilistic sampling density [default: off].
.B [Default: -1]
.SS Output Options
.TP 5
\fB\-\-output-root\fR \fI<string>\fR, \fB\-O\fR \fI<string>\fR
Root directory for all output files.
.B [Default: NONE]
.TP 5
\fB\-\-output\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output filename for groupwise registration archive.
.B [Default: "groupwise.xforms"]
.TP 5
\fB\-\-output-average\fR \fI<string>\fR
Output filename for registered average image.
.B [Default: "average.nii"]
.TP 5
\fB\-\-no-output-average\fR
Do not write average image.
.TP 5
\fB\-\-average-cubic\fR
Use cubic interpolation for average image (default: linear)
.SS Image Options and Operations
.TP 5
\fB\-\-force-background\fR \fI<integer>\fR, \fB\-B\fR \fI<integer>\fR
Force background pixels (outside FOV) to given (bin) value.
.B [Default: disabled]
.TP 5
\fB\-\-histogram-bins\fR \fI<integer>\fR, \fB\-H\fR \fI<integer>\fR
Set number of histogram bins for entropy evaluation.
.B [Default: disabled]
.TP 5
\fB\-\-crop-histograms\fR
Crop image histograms to make better use of histogram bins.
.TP 5
\fB\-\-match-histograms\fR
Match all image histograms to template data (or first image, if no template image is given)
.TP 5
\fB\-\-repeat-match-histograms\fR
Frequetly repeat histogram-based intensity matching to account for changing volume proportions.
.TP 5
\fB\-\-smooth-pixels\fR \fI<double>\fR
Sigma of Gaussian smoothing kernel in multiples of template image pixel size
.B [Default: disabled]
.TP 5
\fB\-\-smooth-cps\fR \fI<double>\fR
Sigma of Gaussian smoothing kernel in multiples of control point delta
.B [Default: disabled]
.SS Transformation Parameters
.TP 5
\fB\-\-grid-spacing\fR \fI<double>\fR
Control point grid spacing.
.B [Default: 40]
.TP 5
\fB\-\-grid-spacing-fit\fR
Use grid spacing that fits volume FOV
.TP 5
\fB\-\-refine-grid\fR \fI<integer>\fR, \fB\-r\fR \fI<integer>\fR
Number of times to refine transformation grid [default: 0].
.B [Default: 0]
.SS Transformation Constraint Options
.TP 5
\fB\-\-zero-sum\fR, \fB\-z\fR
Enforce zero-sum computation.
.TP 5
\fB\-\-zero-sum-no-affine\fR
Enforce zero-sum computation EXCLUDING affine components.
.TP 5
\fB\-\-normal-group-first-n\fR \fI<integer>\fR, \fB\-N\fR \fI<integer>\fR
First N images are from the normal group and should be registered unbiased.
.B [Default: 0]
.TP 5
\fB\-\-zero-sum-first-n\fR \fI<integer>\fR, \fB\-Z\fR \fI<integer>\fR
Enforce zero-sum computation for first N images.
.B [Default: disabled]
.TP 5
\fB\-\-jacobian-weight\fR \fI<float>\fR, \fB\-J\fR \fI<float>\fR
Weight for Jacobian volume preservation constraint [default: off]
.B [Default: 0]
.TP 5
\fB\-\-bending-energy-weight\fR \fI<float>\fR, \fB\-E\fR \fI<float>\fR
Weight for grid bending energy regularization constraint [default: off]
.B [Default: 0]
.SS Optimization Parameters
.TP 5
\fB\-\-exploration\fR \fI<double>\fR, \fB\-e\fR \fI<double>\fR
Exploration of optimization in pixels
.B [Default: 0.25]
.TP 5
\fB\-\-accuracy\fR \fI<double>\fR, \fB\-a\fR \fI<double>\fR
Accuracy of optimization in pixels
.B [Default: 0.01]
.TP 5
\fB\-\-step-factor\fR \fI<double>\fR, \fB\-S\fR \fI<double>\fR
Step factor for successive optimization passes
.B [Default: 0.5]
.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]
.TP 5
\fB\-\-partial-gradient-thresh\fR \fI<float>\fR, \fB\-p\fR \fI<float>\fR
Threshold factor for partial gradient zeroing [<0 turn off]
.B [Default: 0]
.TP 5
\fB\-\-activate-uninformative\fR
Activate potentially uninformative control points
.TP 5
\fB\-\-disable-cp-mask\fR \fI<string>\fR
Path to mask image (matching template grid) defining areas in which control points should be disabled. This guarantees that mask foreground areas remain undeformed.
.B [Default: NONE]
.TP 5
\fB\-\-disable-optimization\fR
Disable optimization and output initial configuration.
.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.