Hi Tim,

> Are these statistics valid?

You seem to have a simple case of traditional paired t-test. You could verify the 3dLMEr result with, for example, 3dttest++.

> How would I arrive at a rational statistical threshold for the mean functional connecitivity maps? the p-value of these
> maps is 1x10^-12 and the cluster extent is 54 mm^3 (2 voxels in real space).

Rationality is in the eye of beholder! I don't take the voxel-wise p-value and the cluster threshold too seriously. If possible, a region-based approach might be more preferable at least for two advantages: 1) avoid spatial boundary ambiguities, and 2) focus on effect estimation instead of dichotomania.

Gang