Thanks so much, this worked perfectly.

I'm looking at the output for the statistics and trying to get an idea of how to interpret it. If this is my output:

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Design matrix = [ ADHD ASD intercept]

Contrast 1: [1 1 0]
Significant findings for Contrast #1
Characteristic Path Length (thresholded matrices, network-wide, negative weights):
beta stat crit_val p corrected p had NaN had imag had Inf
0.0226 3.5502 3.1432 0.0332 0.9958 0 0 0
Characteristic Path Length (thresholded matrices, network-wide, negative weights, excluding disconnected matrices in AUC):
beta stat crit_val p corrected p had NaN had imag had Inf
0.0226 3.5502 3.1432 0.0332 0.9958 0 0 0
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For that thresholds do these p-values apply to or is this an average over all the thresholds? I ran the network calculations over the default sets of thresholds using the second option (same densities).