Hi All,

I have a couple questions for a 2 x 2 repeated measures ANCOVA design. I'm investigating functional connectivity (FC) changes in ROI-to-ROI analysis by choosing 'Select all' to explore the an entire connectome. I've chosen a set of ROIs to be tested as seeds and targets. At the second level, I'm correcting using FDR. At the moment I have used the same set of ROIs to investigate main effects/interaction in both factors as there are antcipated effects in areas common to both factors. 

1) Can I specify a set of targets using the 'select all' instead of the entire brodmanns or harvard atlas'? (I understand this tests all possible connections between seeds/targets with FDR correction)
2) If I expect that FC changes may occur in different areas depending on the factor then can I use a different set of ROIs for different main effects a priori OR should I perform an initial ANCOVA with common ROIs and then post-hoc ANCOVAS? How do you suggest I proceed?

Best,
Michael