SYNOPSIS

lsba [options] targetImage atlasIntensity1 atlasLabels1 [atlasIntensity2 atlasLabels2 [...]]

DESCRIPTION

This tool combines multiple multi-class segmentations from co-registered and reformatted atlases using locally-weighted Shape-Based Averaging.

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).

Input Options

--set-padding-value <double>

Set padding value for input intensity images. Pixels with this value will be ignored. [Default: disabled]

Label Combination Options

--patch-radius <none>

Radius of image patch (in pixels) used for local similarity computation. [Default: 5]

--search-radius <none>

Search radius for local image patch matching. The algorithm finds the best-matching patch within this radius by exhaustive search. [Default: 0]

--no-local-outliers

Detect and exclude local outliers in the Shape Based Averaging procedure.

--no-global-outliers

Detect and exclude global outliers by removing poorly correlated atlases prior to local SBA procedure.

Output Options

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

File system path for the output image. [Default: lsbo.nii]

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.