Greetings!

I am wondering which statistical model is optimal to use for my repeated measures analysis on resting state functional connectivity data. 

My dataset contains 12 subjects, each with 7 sessions (all in the resting state). I have 11 ROIs. I am interested in examining the changes in functional connectivity between sessions, and am wondering what the best statistical test to use is. Using the NYU dataset batch script as a template, I have (1) estimated the first-level seed-to-voxel connectivity maps (bivariate correlation) for each of ROIs, separately for each subject and for each of the 7 sessions, and (2) estimated second-level seed-to-voxel results for each of the ROIs, collapsed across the 7 sessions for each subject. 

I am wondering if it would be better to perform the second level analysis using Conn, or if it would be better to enter the first-level connectivity maps into SPM for more advanced second-level analyses, such as a full or flexible factorial statistical test? 

Thank you!
Kaitlin