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Dear FreeSurfer experts,

I found out that when resampling the LGI maps on the fsaverage6 template, the midbrain is not masked out (i.e., there are LGI values where there should not be any gyrification). Is there a quick way to mask out those regions from the maps? Alternatively, I thought about picking a threshold using the fsaverage6 ?h.thickness in Freeview. However, in this case, I have two questions: how can I read the thickness file as matrix in Matlab (the load_mgh obviously doesn't work), and do the thickness vertices have the same coordinates as in the LGI maps?

Thanks a lot for your support!

Best

Rachele