Hi Lei
There error you are getting is related to the atlas that you are using.
so
a)Is there a folder /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_skull/
b) Is there a folder /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_stripped/ ?
c) do they contain correct ABC atlas data (files 1.mha, 2.mha etc and template.mha)

d) the tissue segmentation directory seems to be missing a "/" at the end. Can you add that and try again?

Martin