Hi Saqib,

yes - design matrix and contrasts look correct. 

You can use [-1 1] and [1 -1] to test for MCI>CN and MCI<CN respecitvely. 

It is possible that more than one subnetwork is found. 

I recommend checking out the NBS manual as well as previous papers that have performed post hoc analyses on subnetworks. 

Best, 

Andrew

Originally posted by Saqib Mamoon:

Hi everyone,

I have recently been introduced to this tool, which greatly interests me. I am sorry if my questions seem silly.

I have directional connectivity matrices with (240 control and 360 MCI) subjects. I want to measure the most significant edges where ( CN > MCI) or (MCI > CN), but I am not very sure how to analyze it. I put all subjects 600 in one folder. I have tried many experiments with varying thresholds from (2.5 to 4.18), sometimes I get a set of only subnetworks, sometimes 2 or 3. I have attached my design matrix. Could you please verify this is correct? 

Summary of my questions.

1) Is the design matrix correct for the task I am trying to do?

2) What does it mean if the tool dNBS outputs one, two, or three subnetworks? How could we analyze them?

3) How to measure the edges with CN > MCI or MCI > CN.

 

Thank you for your valuable time.

 

More info: In the design matrix, the first 360 are MCI subjects, and the next 240 are Normal controls.

Contrast: [-1,1]

signification 0.05

component size Extent

permutations 10k

statistical test t-test