stream_pixels

This tool reads one or more images and writes all their pixels to standard output in binary form. Optionally, each image can be reoriented to a specified anatomical orientation and/or converted to a different data type. This is useful for piping image data through a pipeline, e.g., the Camino DTI toolkit.

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

--reorient <string>: Reorient all images to anatomy-based standard orientation, e.g., RAS or LPS for axial. Default: no reorientation. [Default: NONE]
--change-endian: Change endianness. Default: native endianness.
--convert: Convert data to new scalar type. Default: no conversion. Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", or use one of the following:

--char: 8 bits, signed integer
--byte: 8 bits, unsigned integer
--short: 16 bits, signed integer
--ushort: 16 bits, unsigned integer
--int: 32 bits, signed integer
--uint: 32 bits, unsigned integer
--float: 32-bits, single-precision floating point
--double: 64 bits, double-precision floating point

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

BUGS

Report bugs at http://nitrc.org/projects/cmtk/

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.

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