Hi Lior
it looks like you have significant darkening in the MTL complicated by pretty noisy scans. Can you tell us more about what you are doing? What sequences and scanner are you using? What is your subject population? Control points would probably be your best bet, but this might be able to be improved on the acquisition side as well (although it sounds like it's too late for that)
cheers Bruce
On Tue, 18 Jun 2013, LIOR ZWANZIGER wrote:
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