Hi Allison,
Thank you for using Braph. I hope that you will find it useful during the course of your research.
Regarding the p-values for between group comparison: The fdr column represents the highest p-value that is significant after fdr correction. This value is calculated at a given density, among the multiple comparisons performed between all regions. That is why, when the region changes, the fdr value stays the same. However, since the multiple comparisons are different for each region, the associated uncorrected p-value changes. We discussed this issue previously on this forum and you can find more detailed explanations at: http://braph.org/forums/topic/confidence-intervals-and-p-statistic/ and http://braph.org/forums/topic/eeg-graph-analysis/ .
Regarding the small worldness calculation, you are right. This situation happens when the network is unconnected. Practically, this results in NaN for the path length of the disconnected nodes which then affects the calculation of the mean. To help you with this, could you let me know what type of analysis you are running (weighted or binary undirected (or directed from the command line) so that I can send you a list of changes that need to be done in order to get the harmonic mean.
Hope these explanations help. If you need any additional help, please do not hesitate to ask.
Best,
Mite
