Yes, sure. For example, you can go to Segmentations module and choose to show only the contours. If you are only interested in the brain then you can use Mask volume effect in Segment Editor module to blank out everything else (and then hide the segmentation).
I’m not really sure I follow your instructions. I am trying to view the vessels more clearly, but the mask from the HD brain extraction still overlays my image even though I have the source at top of the entire scan, not the stripped volume. Does that make sense?
