/usr/bin/perl -w =head1 NAME

SYNOPSIS
DESCRIPTION
ARGUMENTS

REQUIRED ARGUMENTS
OPTIONAL ARGUMENTS

EXAMPLE
BUGS
AUTHOR
COPYRIGHT & LICENSE
REVISION
SEE ALSO

SYNOPSIS

display_overlap -roianalysis analysisName -roi roiName -sf sessid -df sessdir [optional arguments]

Type ``display_overlap -man'' for complete documentation

display_overlap displays an overlap map of two or three ROIs. Such a map is created when you run combine_roi with the argument -method overlap. These overlap maps allow you to see exactly what ROIs overlap, where they overlap, and what areas are distinct for each ROI. The Matlab script provides a way to see the name of the ROIs used to create the overlap map as well as a legend of the colors. To find out more information, press h to get a help window.

ARGUMENTS

REQUIRED ARGUMENTS

-roianalysis analysisName: Name of a FSFAST analysis
-roi roiName: Name of the overlap ROI
-sf sessidfile: Name of the session ID file. Note that only one session ID in the file will be used (the last one)
-df sessdirfile: Name of the session directory file.

OPTIONAL ARGUMENTS

-roidir masks: Name of the directory under the analysis roiAnalysisName to hold your ROIs. Defaults to roiAnalysisName_ROI (e.g., for an analysis called ``hfso'', the ROI directory defaults to ``hfso_ROI'').
-base runDirectory: Use this functional directory as the base upon which to display the overlap map. Only needs to be taken into consideration if you used different number of slices or different slice prescriptions for different runs of your scan. Defaults to the first bold directory.
-funcDir bold: Name of the directory holding the functional runs. Usually ``bold'', defaults to ``bold''.
-funcStem fmc: Name of the functional stem from which to create the base. See -base. Defaults to fmc.
-help: Provides complete argument information.
-man: Provides verbose usage information.
-debug: Provides complete debugging information.