.TH average_images "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
average_images \- Average images
.SH SYNOPSIS
average_images [options] image0 ...
.SH DESCRIPTION
This tool computes pixelwiase average, variance, standard deviation, z-score, or entropy images from a list of user-provided intensity images.
.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\-\-mode\fR
Mode of averaging operation
Supported values: "avg", "var", "stdev", "zscore", "entropy", where the default is "avg", or use one of the following:
.RS 5
.TP 5
\fB\-\-avg\fR
Compute average (i.e., mean) image
\fB[This is the default]\fR
.TP 5
\fB\-\-var\fR
Compute variance image
.TP 5
\fB\-\-stdev\fR
Compute standard deviation image
.TP 5
\fB\-\-zscore\fR
Compute z-score image
.TP 5
\fB\-\-entropy\fR
Compute pixel-by-pixel population entropy image
.RE
.SS Data Preprocessing
.TP 5
\fB\-\-log\fR, \fB\-l\fR
Apply log to input data
.TP 5
\fB\-\-abs\fR, \fB\-a\fR
Use absolute input values
.TP 5
\fB\-\-normalize-mean-stdev\fR, \fB\-n\fR
Normalize image intensities using means and standard deviations
.TP 5
\fB\-\-set-padding-value\fR \fI<double>\fR
Define padding value in input images
.B [Default: disabled]
.SS Output Options
.TP 5
\fB\-\-outfile-name\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output file name
.B [Default: "average.nii"]
.TP 5
\fB\-\-type\fR
Scalar data type of output image.
Supported values: "float", "double", where the default is "float", or use one of the following:
.RS 5
.TP 5
\fB\-\-float\fR
Single-precision float.
\fB[This is the default]\fR
.TP 5
\fB\-\-double\fR
Double-precision float.
.RE
.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.