Dear Alfonso,

I'm trying to run a gPPI analysis for 2 groups of patients (drug and placebo group) who scanned two-times (pre/post), each time point has 2 runs and 4 conditions. briefly, it should be a 2(group)-by-2(time point)-by-4(conditions) design.

I preprocessed the pretreatment and posttreatment data with CONN separatly, within which i defined 2 sessions per subject for 2 runs and added the corresponding functional and anatomical images. Everything works well, i got the first level beta map for each patient during each time point and each condition. 

Then i realized that i could not preform the second-level analysis (group-by-time interaction, main effect analysis) with CONN, since i processed the 2 time point data separately.  I then used SPM 12 to do the second-level analysis; i performed a 2(group)-by-2(time point) full factorial design using the beta maps from condition 2 (the most interested condition) derived from CONN to examine the treatment effect on functional connectivity. Finally, i got significant interaction effect and main effec of group after FWE correction.

I wanted to know if it was correct to preprocess the 2 time point data separately and then perform the second level analysis with SPM like i did above? If i was wrong, what should i do?

Best wishes,
Lu

Does anybody has any suggesstion about longitudinal gPPI with CONN?