fslmaths заполняют отверстия

# fslmaths can fill holes in a binary mask.
# `-fillh`: fill holes in a binary mask (holes are internal - i.e. do not touch the edge of the FOV) 
# `-fillh26`: fill holes using 26 connectivity  (it'll fill more vigourously)
fslmaths lesion -fillh lesion
Troubled Tapir