Masking out the cerebellum?

Hi,

I have preprocessed 64 subjects using the CONN default preprocessing pipeline. 
The lower part of cerebellum has been cut off in the QA normalisation with MNI boundary. (see attached)
When I checked each subject, it seems like the areas were not obtained during the scan.

Should I mask this part out? or leaving as it is shouldn't be an issue? 
If I need to mask this out, what steps should I follow to do this properly?

Any suggestions would be much appreciated.

Kind Regards,

Julia Yang