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stream_pixels(1) The Computational Morphometry Toolkit stream_pixels(1)


stream_pixels - Stream pixel data from one or more images to Standard Output.


stream_pixels ImagePaths


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.


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

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
Write the current command line to standard output.
Set verbosity level.
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

Reorient all images to anatomy-based standard orientation, e.g., RAS or LPS for axial. Default: no reorientation. [Default: NONE]
Change endianness. Default: native endianness.
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:
8 bits, signed integer
8 bits, unsigned integer
16 bits, signed integer
16 bits, unsigned integer
32 bits, signed integer
32 bits, unsigned integer
32-bits, single-precision floating point
64 bits, double-precision floating point


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



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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.

Jul 7 2024 CMTK 3.3.1p2