Thanks, Gang.

I was specifically requested to show "group x condition/scan" interaction, and for it, I thought 3dLME is the option. As you suggested that this can be done by 3dMVM, too, I will take a look at this program.

In FSL, I ran repeated measure for each group, which is simple group paired t-test, as follows:

The first explanatory variable (EV) was for the condition/scan differences [1, 1, 1, .....-1, -1, -1....], and then one extra EV for each subject (if there are 8 subjects, there are EV2-9). Contrast 1 with "1" for EV1 and "0" elsewhere, as well as contrast with 2 with "-1" for EV1 and "0" elsewhere, tested for the paired differences (i.e., Contrast 1 implies Pre-scan > Post-scan; Contrast 2 implies Post-scan > Pre-scan).

This method yielded significant results/clusters (Contrast 2, the increase in local functional connectivity, in a few brain regions) only in the experimental group, and post-hoc analysis (e.g., by SPSS) using connectivity values extracted from these clusters (based on the experimental group) confirmed no significant difference (increase nor decrease) in the control group.

Hence, I expected that 3dLME would yield the effect of group x scan interaction....unfortunately it was not the case, and I wonder why!

Sophia