Thank you so much for your links. I can happily report I have the entire pipeline up and running now.
I do have a follow-up question: My team and I are trying to replicate your connectivity process in FSL (specifically using the bedpostx and probetrackx processes). We’ve been trying to use the JHU ICBM normative DTI Atlas for this replication (we don’t have DTI data for our own study because we are looking at patients post-electrode implantation), but it lacks the bval and bvec data necesarry to run the analysis. We were also hoping to use your data in the FSL pipeline, but your connectome files are in .mat format and can’t be used in the FSL environement. Our questions are how you condensed the connectome datasets into .mat files, and if there was a way to use your connectomes in FSL.