I thought I would post this question I received via email in case others have a similar question:
Q: I was wondering if there is a modification that can be made to report the roi (bwMask) not as a binary, but with the original signal intensities of the image?
A: The nice thing about returning the ROI as a logical is that it can be used to index the original matrix directly. So if your original image was I, you can call
>> Iselected = I(bwMask);
to get a vector of signal intensities corresponding to the ROI. Or to get an image with the non-ROI pixels zeroed out, you could call
>> Imasked = I.*bwMask;
For more, see Steve's blog: http://blogs.mathworks.com/steve/2008/01/28/logical-indexing/