I would like to run a functional connectivity ROI-to-ROI analysis with AFNI (first level analysis).
First, I would extract the mean value of the seed-ROI in each subject.
Then, I would calculate FC between these seed-ROI values and the 250 EPI volumes masked by the target-ROI.
Should I use the 250 EPI volumes that are masked by the target-ROI with smoothing?
Or is it better to do the correlation with these volumes without smoothing?
And finally, to be sure, I shouldn’t apply smoothing before calculating the mean values of the seed-ROI, right?
Thank you in advance!