Dear @Raymundo.Cassani I really appreciate you providing this, I have adapted my script, Yesterday I was trying to manually modify the structure according to https://neuroimage.usc.edu/forums/t/scripting-deepatlas-select-deep-structures/9661/2 of the merged surfaces and saving it back to the brainstorm, but somehow brainstorm didn't accept the new modified Atlas, But this totally works!
Best
Erfan