Dear Alfonso,

Thanks a lot. I need again to use this trick because there were minor differences in field of view and voxel sizes between the pre- and post- rsfMRI acquisitions, and therefore I cannot consider them as two sessions in CoNN because the Realign step will fail. I will therefore run all scans as if it was a cross-sectional study and then run a paired t-test as you suggested. However I wonder how could I perform a 2x2 ANOVA in this setting, i.e. how can I find those regions were group A had larger increases/decreases in connectivity (pre vs post) with respect to group B? I guess playing with zeros and ones may do the trick but I am unable to figure it out!
Thanks a lot in advance!