Also check out
http://www.mathworks.com/matlabcentral/newsreader/view_thread/295305#792594
By the way, a circle detection m-file was submitted last week to the
File Exchange:
http://www.mathworks.com/matlabcentral/fileexchange/9168-detect-circles-with-various-radii-in-grayscale-image-via-hough-transform
Now, you said you automatically detected the circular ROI's in the
image. HOW did you do that? Do you have a binary image as a result
of doing that? The binary image will be true or false depending on if
the pixel is in or out of the regions you identified. But you need to
finish your question. What are you going to do with the pixels inside
the ROI's after you've identified them. THAT'S the important part,
and where you could go wrong if you don't do it correctly. Are you
going to mask the image? Crop it? Measure the original image
properties inside the circles? What?
-ImageAnalyst