.TH ttest "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
ttest \- T-tests
.SH SYNOPSIS
ttest [options] imageX0 [imageX1 ...] -- imageY0 [imageY1] ...
ttest [options] --symmetric imageX0 [imageX1 ...]
.SH DESCRIPTION
Pixelwise tests of statistical significance. Also compute correlations and z-scores
.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\-\-log\fR, \fB\-l\fR
Use log data for testing
.TP 5
\fB\-\-abs\fR, \fB\-a\fR
Use absolute data for testing
.TP 5
\fB\-\-abs-out\fR, \fB\-A\fR
Generate absolute (unsigned) data
.TP 5
\fB\-\-invert\fR, \fB\-i\fR
Invert data, i.e., subtract from 1.0
.TP 5
\fB\-\-short\fR, \fB\-s\fR
Convert probabilities to short (and scale by 1000)
.TP 5
\fB\-\-paired\fR, \fB\-p\fR
Compute paired t-test [default: groupwise]
.TP 5
\fB\-\-cross-correlation\fR, \fB\-c\fR
Compute paired cross-correlation
.TP 5
\fB\-\-zscores\fR, \fB\-Z\fR
Compute z-scores of test (y) distribution averages
.TP 5
\fB\-\-text\fR, \fB\-t\fR
Text file input and output rather than image files.
.TP 5
\fB\-\-mask\fR \fI<string>\fR, \fB\-m\fR \fI<string>\fR
Mask file name
.B [Default: NONE]
.TP 5
\fB\-\-outfile\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output file name
.B [Default: "ttest.nii"]
.TP 5
\fB\-\-tstats-file\fR \fI<string>\fR
T-statistics output file name (for correlation: p-value output file)
.B [Default: NONE]
.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.