The research scans use 3D T1 (and sometimes T2) scans for mapping the functional data onto a brain region. They have to put the low res functional scans onto something that has some degree of resolution. Functional scans are acquired with temporal resolution in mind - the change in signal after activation is something like 6 seconds, and to accurately sample this you want a whole brain acquisition in much less time that that. We typically acquire whole brain scans in something like 3 seconds. New techniques such as multiband imaging are acquiring whole brain scans in 600-700ms or so. This is pretty fast.
Clinical scans do use 3D techniques but tend to go for 2D scans (which are a slice, then a gap of 10-30% usually of slice thickness) then a slice.
2D scans are faster, have much better in plane resolution (lower through plane as slices are fatter and have gaps between them). Clinical scans are also one hell of a lot better for identifying things as numerous image weighting a are obtained. MR tech here.