Dear Manja,
It is statistically valid for the threshold suggested by FDR to vary in the different hemispheres. The reason is that FDR defines a proportion, not an absolute. The FDR procedure suggests a p-value threshold with the property that of all positive results at that threshold, one can expect that no more than X percent are false positives (where X is the desired FDR rate). It is very possible that the threshold with this property would be different in the right compared to the left hemisphere.
More informally, one is claiming that of all results declared "significant", X% are probably B.S. Since X is presumably small and the number of results large enough to be interesting, one can safely conclude that the experimental condition explains cortical variation at (most of) the locations indicated. Now divide the brain into subregions (perhaps right and left hemisphere, or perhaps something else) in each of which X% of the significant results are probably false. Then the claim that "X% of the overall results are probably false" is valid.
+glenn
------------------------------------ Here miracles become marvels, and marvels recurring wonders. -- William Beebe
Dr. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl