Dear Alfonso, 

Thanks for your reply.

Does CONN run the single normalization step jointly across both sessions after preprocessing (during the Setup processing pipeline)?

My data were preprocessed via fMRIprep and we also applied ICA-AROMA denoising (data were smoothed ([6 6 6]) before it). However, I preprocessed my baseline and follow-up data separately since I received them at different times. I will preprocess my baseline and follow-up data together (as longitudinal data with the flag of "--longitudinal"), and see if it solves the problem.

While comparing topological changes over time, options (2) and (3) generate similar results. However, the differences are higher when looking at Z matrices. For example, Z(1:7,1) is [1, 0.4594, -0.1653, 0.0050, 0.0533, 0.1107, -0.3014] while using option (2), and option (3) generated [1, 0.5467, -0.0929, 0.1870, 0.2023, 0.2836, 0.0966] for the same data.

In addition, I have another question. We are also interested in the difference between healthy controls (only baseline data available) and patients at follow-up. In this case, should I import data preprocessed jointly or separately?

Best regards,

Chih-Hao