Dear experts,

It's my first time doing longitudinal analysis with CONN.

According to previous replies to the setting for longitudinal studies, there are 2 approaches.

1:  Enter the different sessions as if they were different subjects (https://www.nitrc.org/forum/forum.php?th...)

2: Enter 2 as the "number of sessions" per subject (https://www.nitrc.org/forum/message.php?... https://www.nitrc.org/forum/message.php?...)

I thought that CONN would generate the same ROI-to-ROI matrices with both approaches since I extracted these matrices from the result of 1st level analysis. However, I got different correlation matrices (Fisher's Z values, extracted from "resultsROI_Subject00*_Condition00*.mat") for my follow-up data.

I tested 4 different settings:

(1) Import HC and patient data at baseline, each subject has 1 session

(2) Import baseline and follow-up data (patients only) as different subjects (e.g. import baseline data as Subject 1-10, and then import follow-up data as Subject 11-20)

(3) Import baseline and follow-up data (patients only) as 2 sessions for 1 subject. Each subject has 2 sessions: baseline and follow-up

(4) Import follow-up data only, each subject has 1 session. 

While comparing the Z matrices for baseline data, (1), (2), and (3) generated the same matrices. However, while focusing on follow-up data, (3) generated different correlation matrices, compared with (2) and (4). 

I plan to extract ROI-to-ROI matrices for other analyses (e.g. graph theory), but I', confused about which setting I should use for my longitudinal data. Does anyone know which one is the better approach?

Best regards,

Chih-Hao