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average_images(1) The Computational Morphometry Toolkit average_images(1)


average_images - Average images


average_images [options] image0 ...


This tool computes pixelwiase average, variance, standard deviation, z-score, or entropy images from a list of user-provided intensity images.


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

Mode of averaging operation Supported values: "avg", "var", "stdev", "zscore", "entropy", where the default is "avg", or use one of the following:
Compute average (i.e., mean) image [This is the default]
Compute variance image
Compute standard deviation image
Compute z-score image
Compute pixel-by-pixel population entropy image

Data Preprocessing

Apply log to input data
Use absolute input values
Normalize image intensities using means and standard deviations
Define padding value in input images [Default: disabled]

Output Options

Output file name [Default: average.nii ]
Scalar data type of output image. Supported values: "float", "double", where the default is "float", or use one of the following:
Single-precision float. [This is the default]
Double-precision float.


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