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I found all the existing atlas with .aseg (subcortical components) contains only structures can be allocated in left/right lobe. Is there any required modification for use custom atlas with structure cannot be assign left or right? (i.e. brainstem, pons)

Should I just put 3rd value (like M for middle instead of L or R) in column? It seems empty column causes error.

You can try using 'B' for "both"; I think that was used for some other atlases.