There's a lab at UCSF[1] that actually specializes in doing genome sequencing of cerebrospinal fluid specifically for cases like this. They're talked about pretty extensively in Adam Savage's "Still Untitled" podcast[2] and all the crazy weird things they managed to diagnose this way.
We all have the impression that medicine is a solved problem, but we've still got a way to go. We're still making progress though.
[1] https://nextgendiagnostics.ucsf.edu/
[2] https://www.tested.com/podcasts/adam-savage-project/854328-s...
We just have a few pieces of a puzzle and no idea what the overall image actually is. Neuroplasticity and adaptivity make this even harder because often you can't just take a part away like in a car and pinpoint issues due to the absence or disturbance of these parts.
If you knockout an area and a patient loses smell, will you say that you found the "center" of smell? We are still poking at the brain and figuring out its responses.