[Freesurfer] Temporal Lobe Problem

Hi, I have scans of around 60 participants and about 75% percent of these have significant portions of their temporal lobe excluded. I have attached different slices from four different subjects to give you an idea of the typical scan I've been encountering, [though there are problems in minimally 10 slices for each participant and some exclusions can be found in more than 50 slices.] We are using FreeSurfer version 5.1.0. What is your advice, since there are so many slices for a large number of participants that would need to be edited? Extension of the watershed parameters, adding control points, or something else I haven't considered? I am hesitant to add control points for such a great number of participants. Thank you! Lior Zwanziger