SYNOPSIS

reorient [options] new-orientation infile outfile

DESCRIPTION

Convert between image orientations, i.e., physically re-order pixel array and adapt stored anatomical orientation information

OPTIONS

Global Toolkit Options (these are shared by all CMTK tools)

--help

Write list of basic command line options to standard output.

--help-all

Write complete list of basic and advanced command line options to standard output.

--wiki

Write list of command line options to standard output in MediaWiki markup.

--man

Write man page source in 'nroff' markup to standard output.

--version

Write toolkit version to standard output.

--echo

Write the current command line to standard output.

--verbose-level <integer>

Set verbosity level.

--verbose, -v

Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>

Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

--input-orientation <string>, -i <string>

Override input orientation. This is a three-letter code, e.g., 'RAS', 'LPI', etc. [Default: NONE]

--output-orientation <string>, -o <string>

Override output orientation. Default is 'RAS', or the closest match supported by the output image file format [Default: NONE]

--output-space <string>

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. [Default: NONE]

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

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.