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What was the reason for using a density scanner then throwing GPUs at it, rather than just using a scanner that worked, such as 13C MRI ?

MRI ought to produce better results. But do we have high-enough-resolution MRI scanners?

I was under the impression that you can always get more resolution out of MRI by scanning for longer and giving the machine more compute and RAM.

Has MRI actually been proven to work with similar carbonized scrolls ?

MRI has proven useful when the ink was made with iron compounds ("oak-gall ink"). But that was used mostly starting a few centuries later.

These scrolls use carbon-based ink with composition much like the paper. But there might still be usable differences.