.TH reorient "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
reorient \- Reorientation
.SH SYNOPSIS
reorient [options] new-orientation infile outfile
.SH DESCRIPTION
Convert between image orientations, i.e., physically re-order pixel array and adapt stored anatomical orientation information
.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\-\-input-orientation\fR \fI<string>\fR, \fB\-i\fR \fI<string>\fR
Override input orientation. This is a three-letter code, e.g., 'RAS', 'LPI', etc.
.B [Default: NONE]
.TP 5
\fB\-\-output-orientation\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Override output orientation. Default is 'RAS', or the closest match supported by the output image file format
.B [Default: NONE]
.TP 5
\fB\-\-output-space\fR \fI<string>\fR
Override output coordinate space (e.g., 'RAS', 'LAS', 'LPS'). This does not affect the array order. Default is to write image in the input image space.
.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.