cmtk-sba(1) [debian man page]

sba(1)						       The Computational Morphometry Toolkit						    sba(1)

NAME

       sba - Shape-based Averaging of label images

SYNOPSIS

       sba InputImageVector

DESCRIPTION

       Average segmentations (label fields) using the Euclidean Distance Transform. All input images must be in the same space. EDT is computed in
       this space also. See http://dx.doi.org/10.1109/TIP.2006.884936 for details of the underlying algorithm.

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
       --num-labels <integer>, -n <integer>
	    Number of labels. It is assumed that only values [0..num] occur in the images [Default: 0]

       --padding <float>, -p <float>
	    Padding value in input image [Default: disabled]

   Label Combination Options
       --exclude-outliers, -x
	    Exclude local outliers in the shape-based averaging algorithm. Outliers at each pixel are defined as those input images for which  the
	    distance from the nearest pixel with the current label exceeds thresholds computed from the set of distances over all inputs.

   Output Options
       --output <string>, -o <string>
	    File name for output segmentation file.  [Default: sba.nii ]

AUTHORS

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

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From  April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 							    sba(1)

lsba(1) 					       The Computational Morphometry Toolkit						   lsba(1)

NAME

       lsba - Local voting.

SYNOPSIS

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

DESCRIPTION

       This tool combines multiple binary 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, and Daniel B. Russakoff

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging  and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 							   lsba(1)