Brain scans are not as accurate as one might think. Most or all methods merely show activation of neurons or groups of neurons over a timescale.
Typically you give a person, say a memory task, you look at which areas fire up as he tries to memorise a word list and from that you extrapolate whatever you can from it.
I also believe working memory and short term memory are to some extent better understood than long term memory. actually the least known process regarding memory I think is how memories pass from working memory or short term memory into long term memory.
