Hi pt,

Thanks for your input.

My research needs to do a topography analysis:

within each cluster, I calculate the feature distance and Euclidean distance between pairs of nodes and try to identify if there is a relationship between a physical map and a feature map. In this way, this flat map distance, which should correspond to surface distance, is more appropriate than the anatomical map in a 3D brain. I'm actually doing the thing you suggested: create the flat map first and project my data to the flat map...and some clusters got cut into halves.

What do you mean by 'calculating along the anatomical surface'? It sounds like the same thing I'm trying to do but I don't know how to directly calculate the surface distance without flattening it into a flat map.

So for my analysis, the inter-cluster distance doesn't matter, what matters is the nodes' relative position to each other within a cluster. The only reason I'm proposing the avoid-cluster cuts is because it will cause the error and I couldn't run surfclust.