James,

A couple of comments-

1) To avoid any double-dipping accusation, it would be better to just run voxel-wise analysis on the whole brain instead of focusing on individual ROIs. With a one-way repeated-measures (or within-subject) ANOVA with three levels, you can simply run three separate paired t-tests, which can also be obtained through -adiff or -acontr in 3dANOVA2.

2) The phrase "significantly different" in your description should be interpreted in the statistical, not practical, context. What this means is that "HC and LC are significantly different from 0" is meaningful because there is a significance level (like a p-value) associated with it. However, "the differences between LC and NC are not significantly different from 0" is *not* meaningful even though everybody seems to know what you mean! What I'm trying to say is that, the practical difference LC and NC could be big (e.g., 0.65% signal change) but that difference might have failed to reach a desired significance level due to power issue or some other reasons. So it would be difficult to statistically show the equality part in the relationship "HC > LC = NC".

3) For this part:

> we would like to show that not just is LC vs NC nonsignificant in one cluster and
> significant in another but that this difference is itself significant.
> Can we use a paired t-test to show that the LC > NC differences are themselves
> significantly different? Or just run a 2x2 (or 2x3 if there are three regions) ANOVA?

it seems that you want the interaction effect from a 2x2 within-subject ANOVA with two factors, condition and region. Then you can claim the contrast between the two conditions at one region is greater than the other region at a designated significance level. Again be careful about statements like "LC vs NC nonsignificant in one cluster".

Gang



Edited 1 time(s). Last edit at 03/31/2016 06:36PM by Gang.