Dear Dr. Zalesky,

Thank you to you and your collegues for the wonderful tools and toolboxes you have given the neuroscientific research community!

I've been working with the NBS toolbox for most of the day, and while I have made great progress in understanding what I am doing, I'm still unsure about which design matrix to use (I've made quite a few).
The help section for statistical model was very useful, but after creating several different matrices and analyses, I'm still unsure which is correct.

Simply put, I have 48 matrices belonging to 12 participants (within subjects design). They were tested on 2 seperate days (Placebo vs Drug) and had two resting state scans on each day (No music vs Music). The order of the matrices (90x90x48) is as follows:


S01 Placebo No-music (0 0)
till
S12 Placebo No-music (0 0)

S01 Placebo Music  (0 1)
till
S12 Placebo Music (0 1)

S01 Drug No-music (1 0)
till
S12 Drug No-music (1 0)

S01 Drug Music (1 1)
till
S12 Drug Music (1 1)

I am interested in the main effects of drug and music, but more specifically in the interaction effect between drug and music (and subsequently visualizing this in BrainNet). Using FDR there are barely any suriving edges, and the NBS seems perfect for situations like these.

My main issue has been the design matrix. As pictured above, I initially had a simple 48x2 with 1s and 0s (and later 1 and -1), but was consistently getting 1000s of significant edges for certain thresholds (so clearly not looking at the specific interaction). Could you tell me the dimensions of the required/recommended design matrix? I've attempted a 48x3 for A, B and AxB, 48x5 for A1, A2, B1, B2, AB, but am confused about the requirement of a column for each participant?

If someone here could provide me with some tips/pointers about the required dimensions for the matrix, the interaction contrast, and how the first line in the matrxi would look, I'm sure I can figure out the rest through deductive reasoning. Any help would be greatly appericiated.

Sincerely,

David

ps. Would you recommend using raw R values or Fisher Z transformed R values?