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To be honest, I had exactly the same thought. 

For example, by some chance, do the pages that you want to annotate consist of a lot of graphics, and the vocabulary of the text is esoteric (eg, a medical textbook), so you just scan or photograph the pages, but putting them through an OCR program would result in too many errors and hence the whole process would become very labor intensive?    So, as Mark said, a bit more background info would be very helpful in guiding you.

 

Cheers,

 

Tom M