Hi Rob,
So I just tried your approach and up until the “overlapping mask labels” part it, all worked out quite well. Indeed the outcome looks a bit “speckly” but for now that is absolutely fine I think. I just had some trouble understanding the code from line 2301 on. From what I understand, the first mrcalc command calculates the cortical overlap between the two hemispheres, the second mrcalc (line 2308) does the same for the subcortical areas and with the final mrcalc (line 2319) the three .mgz files (lh, rh, subcortex) are merged and output as “aparc.BN_Atlas+aseg.mgz”, taking into account potential overlap. Is this (somehow) correct, or am I completely on the wrong track here?
Also, if I am just interested in the cortical parcellation (BN Atlas 210), may I just leave out the second mrcalc command (line 2308)?
Thank you very much for your help! It is the first time, since a few days, that I finally make some progress with the BN Atlas.
Best regards
Lars