Dear Andrew, 

I have a query about NBS set-up and want to confirm if my interpretation. After reading the manual & a lot of posts on this forum, I am not certain if my method is correct. 

My hypothesis: I am looking if there is a difference between healthy controls and patients, in functional connectivity (source EEG -> imaginary coherence). 

My doubts: I don't know if my contrast is set-up correctly; and therefore if my interpretation of the results is correct.

Design Matrix: My design matrix is as shown. I have 17 controls, 22 patients - so its 39 rows in total and 2 columns.

Statistical Test: t-test

Contrast: [1 1] - im not interested in increase/decrease just the difference in functional connectivity between controls and patients. 

Threshold: 0.5 -to- 22 - I have ran the code for a wide range of threshold values, but even at t=22 I have a large network of significant connections, which to me seems unusual.

Connectivity matrices: These are 68x68 ROI matrices, 39 total - again set up as control 1-17 (total17), patient 18x39 (total22). Diagonal is also '1', just as in the schizophrenia example.

Node Coordinates & Node Labels: separate files, both load in well. Tripled checked these are correct.

Exchange blocks: N/A - not used.

Permutations: 5000

Significance: 0.05

Method: Network-Based Statistics (NBS)

Component Size: I tried both: extent & intensity. 

Question 1: Is my design matrix correct? From the manual and some of the posts on this forum I believe it is suitable for my hypothesis. 

Question 2: What about the contrast? I've set it to [1 1] because im just looking for a difference. However, maybe contrast should be [1 0]?

Question 3: Is my "t" threshold unsually high? At t=22, contrast[1 1] - I get a p-value of 0.035, 55 edges, 39 nodes all over the brain (on intensity setting), but at 22.5 nothing is significant anymore; seems like a very sharp drop aswell.

Thank you for your time! 

Vyte