Dear Jeffrey Spielberg,
Thank you very much for your help. When the design matrix is n*n*number of subjects*conditions, I still cannot figure out the corresponding design matrix and contrast. In your article named "Flexible brain network reconfiguration supporting inhibitory control" which published in 2015 in PNAS, each graph property was entered as a repeated-measure dependent variable into the GTG toolbox, with task condition (incongruent vs. congruent) as the repeated measure. Could you teach me how to write the design matrix and contrast when you analyze the data to compare the two conditions in your article? I mean if you could give me an example like the one below that from NBS.

design matrix:
1 0 0 0 1
0 1 0 0 1
0 0 1 0 1
0 0 0 1 1
1 0 0 0 -1
0 1 0 0 -1
0 0 1 0 -1
0 0 0 1 -1
contrast:
0 0 0 0 1

Thank you again. I am looking forward to hearing from you.

Best wishes,
xiuling