Landmarkmatch - lesion mask?

[arianayoum]

Right now I am using the landmarkmatch script to register my T1 to a template with hippocampal areas being the landmark.
However, some of my brains have missing tops due to a scanning error so I want to add in a lesion mask.

1. Is there a way to create this lesion mask using ANTs?
2. How should I add in this lesion mask to my landmarkmatch script?

Thank you!