Hi,

Sorry I should have given more details. But yes, you comfort what I was thinking about negative values.

So more details. I have a group of 61 subjects with acquisition at 3 time points (6months, 36months and 60months respectively M6, M36 and M60).

So I use the fsl (feat) website to create my design matrix. Here is an example for 2 subjects:

 1  1 1 0
 1  1 0 1
-1  0 1 0
-1  0 0 1
 0 -1 1 0
 0 -1 0 1

With the two first columns coding the timepoints and the 2 last for the subjects
So one of my contrast to get M6-M60 is [1 2 0 0].

Basically,  I ran that design on NBS (with nbs stat, a t-test, 5000 permutations, block exchange 1:61,1:61,1:61 (for my 61 subjects)) and I got stat at 0.054. So close of significance that I decided to try the FDR analysis. I increased the number of permutation to 100000, changed the stat to FDR  (kept the exchange blocks is it right?) and ran it.
It took a long time and I got significant results (for my 3 contrasts M6-M60; M6-M36 and M36-M60).
So my idea to represent them was to multiply nbs.NBS.con_mat with nbs.NBS.test_stat and plot the connection which were not equal to zeros. But here I am getting positive and negative values (even low values) and that for the results of my three contrasts.

I think I must do something wrong, but I  have trouble figuring where.
Thanks a lot for your patience and help.

Cecile