SYNOPSIS
combine_roi -roianalysis roiAnalysisName -inputroi [ROI1,ROI2,ROI3, ...] -outputroi roiName -method <intersection | union | overlap> -sf sessid -df sessdir [-maskdir masks -funcDir bold -force -help -man]
Type ``combine_roi -man'' for complete documentation
DESCRIPTION
combine_roi allows one to combine multiple ROIs together quickly and easily. If, for example, you have ROIs for left and right FFA, and have computed ROI averages for each of those regions, but now want to consider the FFA together, irrespective of hemisphere, you can use combine_roi with the ``union'' method to create a new ROI. As well, if you have an anatomical ROI and a functional ROI, you can use combine_roi with the ``intersection'' method to get a new ROI that is the intersection of those two ROIs. Thus, ``intersection'' is like ``AND'' and ``union'' is like ``OR''.
As well, combine_roi can also be used to create an ``overlap'' ROI. This ROI is specially coded to show how up to three ROIs overlap. This is extremely useful if, for example, you have functionally defined three areas with different tasks and want to know if the areas overlap. To view the results, you can use the program display_overlap.
Note that when giving the list of input ROIs to combine, the names must be separated by commas, with no space in between the comma and the next ROI. See the example below for more details.
ROIs created by combine_roi are viewable and editable using edit_roi.
ARGUMENTS
REQUIRED ARGUMENTS
- -roianalysis roiAnalysisName
- Name of the analysis from which you computed the ROI. Do not use in conjunction with -maskdir.
- -inputROI roiList
- List of ROI names, delimited by commas, e.g., ROI1,ROI2,ROI3. Note that you cannot have a space inbetween the ``,'' and the next ROI in the list.
- -outputROI roiName
- Name of the ROI in which to put the output.
- -method <intersection | union | overlap>
- Name of the method to use when combining the ROIs. ``intersection'' will only consider a voxel to be part of the output ROI if it was in all of the input ROIs, while ``union'' will consider a voxel to be part of the output ROI if it was in any one (or more) of the input ROIs. Thus, ``intersection'' is like AND while ``union'' is like OR.
-
``overlap'' is different than the other two. If you use ``-method overlap'', combineROI will take the input ROIs (to a maximum of three) and compute the areas that are distinct and overlap. The order of your ROIs on the command line determines the colors that are used to determine the distinct and overlaping areas. You can display the resulting map using displayOverlap. The colors are as follows:
-
2 ROIs: blue - condition 1 | red - condition 2 | white - overlap of both conditions
-
3 ROIs: blue - condition 1 | red - condition 2 | yellow - condition 3 | purple - condition 1 and condition 2 | orange - condition 2 and condition 3 | green - condition 1 and condition 3 | white - overlap of all conditons
- -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
- -maskdir masks
- Name of the directory under the bold directory funcDir to hold your ROIs. Defaults to analysisName_ROI, so if your analysis is called hfso, the mask directory would be called hfso_ROI and made underneath the bold directory.
- -funcdir bold
- Name of the directory holding the functional runs. Usually ``bold'', defaults to ``bold''.
- -force
- If an roi named roiName already exists, combineROI will quit. Use this option to override this behavior, but be warned that it will overwrite the existing ROI.
- -help
- Provides complete argument information.
- -man
- Provides verbose usage information.
- -debug
- Provides complete debugging information.
BUGS
None known of. Send bug reports to <froi-bugs@sourceforge.net>.
AUTHOR
Nicholas Knouf, <nknouf@mit.edu>, <nknouf@mimeme.net>
COPYRIGHT & LICENSE
Copyright (c) 2003, Nicholas Knouf, MIT.
This program is free software and is governed by the terms of the Artistic License.
REVISION
$Id: combine_roi,v 1.9 2003/10/06 16:03:46 nknouf Exp $
SEE ALSO
display_overlap, make_roi, edit_roi