Ok. Here goes.
In my opinion, there are six possibilities for the relationship between brain function and thoughts.
1.) Thoughts are brain function.
2.) Thoughts cause brain function.
3.) Brain function causes thoughts.
4.) Something else causes both thoughts and brain function.
5.) There is no relationship.
6.) Brain function sometimes causes thoughts; sometimes thought cause brain function.
We can probably agree that 5 is not worth considering. All the evidence suggests that there is a definite relationship between the two. The fact that machines can use this relationship to read thoughts, if crudely as yet, is pretty much proof that there is a relationship.
I think we can rule out 2 and 4 pretty easily. After all, we know that when we do certain things to the brain - drugs, surgery, damage - thinking changes. The alterations happen first. Therefore, the causal relationship does not flow from thoughts to brain function - at least, some of the time.
Further, this means that the relationship has to be a direct one, not an indirect one as postulated in 4. If something else causes thoughts and brain function (x happens and causes thought Y to happens
and brain function Z to happen) then altering brain function would have no affect on thoughts.
As such we are left with 1, 3 and 6.
Examining 3 - that brain function causes thoughts - we can see that it is a position that is in opposition to both of our particular philosophies. That is no reason to rule it out, but I think we can set it aside for now.
The real dispute between us comes from you supporting position 6 and me supporting position 1.
I will pause there for a moment, as I have to do some work.