Hi Kaitlin,

Typically the "sign" of connectivity is evaluated a posteriori after your statistical inferences (e.g. you find first which regions show differences in connectivity between two subject groups, and then you evaluate whether the found differences relate to positive-connectivity or anticorrelations within each group). If you prefer, instead, to focus your analyses only on those regions that show anti-correlations with your seed you may use a conjunction analysis/mask in order to do that. For example, you may first look at the sign of connectivity with your seed and create a mask of all significantly anti-correlated areas, and then use that mask in SPM when evaluating your effects of interest (e.g. between-group differences) to focus only on those regions. Let me know if you would like me to clarify how to do this.

Regarding the 2nd level beta values, yes, the values in conn_*/results/firstlevel/BETA_Subject#_Condition#_Source#.img wil contain the fisher-transformed correlation values for each subject/condition/seed combination, which can be entered into SPM for additional 2nd-level analyses. 

Hope this helps
Alfonso
Originally posted by Kaitlin Cassady: