Hi! 

I have a question related to random effects and fixed effects on the 2nd level analysis in CONN. I am trying to extract the functional connectivity values between two ROIs in order to perform a mixed model analysis in R. In this analysis, I would normally use subject as a random effect. However, I am uncertain if this is already taken into account in the functional connectivity measures extracted from CONN. Specifically, I would like to know if the intercept is already modeled as a random effect across subjects when using the "subject effects" (e.g., "All Subjects") in CONN (Q1).

Moreover, are the "subject effects" considered random effects and the conditions considered fixed effects in CONN's second-level analysis (Q2)?

Thank you in advance!

Beatriz