It looks like when you use this line:
Vol(Vol(:,:,p) > 0) = 65535
you are in fact referring to a 2D matrix corresponding to a single channel from an image instead of a 3-channel image from your volume. I think it would save you trouble if you used this:
instead of your for-loop, since you would then replace all the pixel values greater than 0 with 65535.
EDIT:
I just saw that you asked this question on Stack Overflow, good idea by the way, and that Ray provided a very thorough explanation! Anyhow I hope it is clearer for you now :)
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