Freesurfer skullstripping error - Freesurfer

30 Nov 2020


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Dear Freesurfer users,
Hope this finds you well.
I preprocessed our dataset with recon-all <subj&gt; -s <subj&gt; -all -qcache and found a number of our subjects had different levels of skullstrip errors. I tried fixing them by a couple of different approaches, such as -gcut and adjusted watershed threshold, but they both failed to fix the overlapping of dura mater (Fig1 and 2). I tried two methods on different subjects and received the same outcome. I wonder if you have any ideas to fix this error. At this point, for some who had less skullstripping, I can erase them manually and run -autorecon-pial or -make. But for the others with multiple locations of skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to them at a systemic level? Also I found the skullstripping error in over half of our subjects, is it normal that we have a such proportion? 
Thank you so much!
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Best regards,
Yezhe
Yezhe Lin, MD MMed&nbsp; (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin.bee@gmail.com
Twitter: @LinYezhe | LinkedIn&nbsp;| Researchgate
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