.TH groupwise_affine "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit" .SH NAME groupwise_affine \- Affine population registration .SH SYNOPSIS groupwise_affine [options] image0 [image1 ...] .SH DESCRIPTION This tool 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\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\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\fR, \fB\-t\fR \fI\fR Input filename for pre-defined template image. .B [Default: NONE] .TP 5 \fB\-\-template-with-data\fR \fI\fR, \fB\-T\fR \fI\fR Use user-supplied template images's pixel data in registration .B [Default: disabled] .SS Output Options .TP 5 \fB\-\-output-root\fR \fI\fR, \fB\-O\fR \fI\fR Root directory for all output files. .B [Default: NONE] .TP 5 \fB\-\-output\fR \fI\fR, \fB\-o\fR \fI\fR Output filename for groupwise registration archive. .B [Default: "groupwise.xforms"] .TP 5 \fB\-\-output-average\fR \fI\fR Output filename for registered average image. .B [Default: "average.nii"] .TP 5 \fB\-\-average-linear\fR Use linear interpolation for average image \fB[This is the default]\fR .TP 5 \fB\-\-average-cubic\fR Use cubic interpolation for average image .TP 5 \fB\-\-no-output-average\fR Do not write average image. .SS Multiresolution Parameters .TP 5 \fB\-\-downsample-from\fR \fI\fR, \fB\-d\fR \fI\fR Initial downsampling factor .B [Default: 4] .TP 5 \fB\-\-downsample-to\fR \fI\fR, \fB\-D\fR \fI\fR Final downsampling factor. .B [Default: 1] .TP 5 \fB\-\-sampling-density\fR \fI\fR, \fB\-s\fR \fI\fR Probabilistic sampling density. Legal values between 0 and 1. .B [Default: disabled] .SS Image Options and Operations .TP 5 \fB\-\-force-background\fR \fI\fR, \fB\-B\fR \fI\fR Force background pixels (outside FOV) to given (bin) value. .B [Default: disabled] .TP 5 \fB\-\-histogram-bins\fR \fI\fR, \fB\-H\fR \fI\fR Manually 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\-\-smooth\fR \fI\fR Sigma of Gaussian smoothing kernel in multiples of template image pixel size. .B [Default: disabled] .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\-\-free-and-reread\fR Free memory allocated for original image whenever these are not needed and re-read image files as needed. This can be useful when running on a machine with limited memory resources. .SS Transformation Parameters .TP 5 \fB\-\-dofs\fR \fI[,,...]\fR Add DOFs to list [default: one pass, 6 DOF] .TP 5 \fB\-\-zero-sum\fR, \fB\-z\fR Enforce zero-sum computation. .TP 5 \fB\-\-normal-group-first-n\fR \fI\fR, \fB\-N\fR \fI\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\fR, \fB\-Z\fR \fI\fR Enforce zero-sum computation for first N images. .B [Default: disabled] .SS Transformation Initialization .TP 5 \fB\-\-align-bounding-boxes\fR Initially align centers of bounding boxes of all images by translations \fB[This is the default]\fR .TP 5 \fB\-\-align-centers-of-mass\fR Initially align centers of mass by translations .TP 5 \fB\-\-init-scales\fR Initialize scale factors using first-order moments .SS Optimization Parameters .TP 5 \fB\-\-exploration\fR \fI\fR, \fB\-e\fR \fI\fR Exploration of optimization in pixels .B [Default: 0.25] .TP 5 \fB\-\-accuracy\fR \fI\fR, \fB\-a\fR \fI\fR Accuracy of optimization in pixels .B [Default: 0.01] .TP 5 \fB\-\-repeat-level\fR \fI\fR, \fB\-r\fR \fI\fR Number of repetitions per optimization level .B [Default: 5] .TP 5 \fB\-\-step-factor\fR \fI\fR, \fB\-S\fR \fI\fR Step factor for successive optimization passes .B [Default: 0.5] .TP 5 \fB\-\-delta-f-threshold\fR \fI\fR Optional threshold to terminate optimization (level) if relative change of target function drops below this value. .B [Default: 0] .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.