Hi Yezhe
It depends a lot on what your resolution, read out direction, bandwidth and
field strength are. We generally fix these with T2 or FLASH scans at the same
resolution/geometry/readout as the T1. Otherwise they are pretty tough as the
dura is close enough to the gray matter that you can’t see any space between
them
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of LIN, Yezhe
Sent: Monday, November 30, 2020 5:10 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer skullstripping error
External Email - Use Caution
Dear Freesurfer users,
Hope this finds you well.
I preprocessed our dataset with recon-all <subj> -s <subj> -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!
------------------
Best regards,
Yezhe
Yezhe Lin, MD MMed (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin....@gmail.com<mailto:yezhe.lin....@gmail.com>
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