Hi Naail,
It isn't exactly the voxel count that is the reason, it is the
very heavy bias in selected voxels. It sounds like you are
running FDR restricted to voxels that have small p-values,
which will almost force such strange results (q ~= p) until
p goes well below the original threshold.
In any case, it does not seem appropriate to run FDR after
thresholding. The FDR mask should be independent of the
tests in question.
- rick