Gang,
thanks for your reply. to answer your questions:
1) Did the family-wise error correction with AlphaSim apply to the F- or t-map, or both?
- The alphaSim corrections would apply to both F and t-maps.
> Reviewers of our paper (who seem to use SPM) are saying that t-tests should
> be not whole brain but should be done only on clusters that were significant in
> the interaction map and different p values should be given for every cluster.
2) I'm confused here: Do you mean the reviewers suggest that only statistical analysis at ROI level (averaged across the ROI?), but not the whole brain, is legitimate?
-kind of, they are basically saying that t-tests should be done only for the significant clusters coming out of the whole brain anova F maps (it seems to me like a ROI approach, too), and I see in papers published by this research group that their tables show different p values for each significant cluster reported in the table, whereas in AFNI I usually report the common corrected p value obtained through AlphaSim. I am not sure if this is just a difference between SPM (with which unfortunately I am not familiar) and AFNI, which uses the AlphaSim approach, or if I am missing something important.
3) One last question: if the whole brain anova shows a significant interaction in the F map (eg, group by Task) is it ok to report this significance by picking one F and p value (eg, "The significant two-way interaction of Group by Task[F(2,53)= 3.93, p= .025] was further explored by conducting pair-wise comparisons to clarify significant within-group and between-group differences due to task condition "), and then move to t-tests results for specific contrasts?
Or what else would I need to report? This is another point that I do not seem to convey clearly to the reviewers, as they think I am just doing t-tests without a whole brain anova.
Thanks a lot!
Alessandra
