Both
Lyme and MS can be diagnosed clinically, based on symptoms
and not just tests. However, owing to advances in MRI imaging, more and more doctors depend on the MRI in diagnosing MS. Likewise, even through their are suspicions about the Lyme blood tests, some doctors still rely on them solely.
Lyme doesn't always cause brain lesions. There are different strains of Lyme, and also different "co-infections," which ticks also carry and transmit.