I've been looking at between-group (controls and disease) differences in cortical thickness cross-sectionally and longitudinally (PC1). I've outputted sig.mgh maps and effect size maps (gamma.mgh) but the cross-sectional gamma.mgh maps are coming up blank. Could you explain why this is (and why it works for the longitudinal data) and how I can create a cross-sectional effect size map? 

As the scans I am an analysing are from four different scanners I am also looking at scanner differences in the controls only. No significant differences are coming up but the effect size maps are showing both positive and negative differences across the whole brain and the gammavar.mgh maps are completely yellow (5 on the colour bar). How do I interpret this? 

Any help would be much appreciated. Thanks,

Elin