How to remove sub-cortical activation

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I'm using the attached code to perform source localization on my resting
state MEG data.
How can I remove activation showing up from sub cortical regions.
The images obtained are transparent and is difficult to identify activation
from which region as the activated area are visible from both sides making
it difficult to differentiate. How can I make the inner surface of brain
opaque.

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Dear Vivek,

It's hard to help you if you give code that we cannot run and you
don't share figure of what you see.

If you still have the problem please try to provide a script that uses
one of the MNE datasets.

http://martinos.org/mne/stable/manual/datasets_index.html

Best,
Alex