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Dear FSL experts, I am starting a resting-state study analysis using a seed-based approach and I would need some basic advice. I am following the standard rules for preprocessing and processing (temporal filter, regressing 9 nuisance variables, etc..) 1. I would like to know if there is a rule (or advice) for the seed dimension. My images are from a 1.5T scanner and have 3mm resolution. In the literature, I have observed that smaller seeds are used for subcortical areas (basal ganglia), but I would need an advice about this point (4mm radius for subcortical areas and 5-6mm radius for cortical areas? is it ok?). 2. I have also observed that many studies did investigate only positive correlations, while others both positive and negative correlations. Is there a rule (advice) about this? 3. again in the literature I have observed that some studies explored the whole-brain functional connectivity of a seed, but also the strength of the functional connectivity between two seeds. which type of information does this analysis add? Which is the best method in FSL to explore the strength of the functional connectivity between two seeds? is it only a problem of masking? Thank you for any help Angela