Hi Freesurfer Users,
I am checking my data and there are many scans with a bit of dura being captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects. I am removing them manually them using Freeview, then running the autorecon-pial. But this will take a lot of time on 200+ subjects.. Does anyone have any tips to deal with these little inclusions? Thanks =)
Best Wishes, Shane
Hi Shane
by far the best way to do this is if you have a T2 or FLAIR scan that is high-enough resolution (i.e. around 1mm isotropic).
If not, you can try the graph cuts skull stripping option in recon-all. It is more aggressive than the watershed (which is the default).
cheers Bruce
On Wed, 12 Apr 2017, Shane S wrote:
Hi Freesurfer Users, I am checking my data and there are many scans with a bit of dura being captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects. I am removing them manually them using Freeview, then running the autorecon-pial. But this will take a lot of time on 200+ subjects.. Does anyone have any tips to deal with these little inclusions? Thanks =)
[8D698381-1005-4719-B2FC-E8C0C496FB50_1_preview.jpg] [EDA1574B-CAF0-45E7-ACDE-CDD777931400_1_preview.jpg] [F256742A-4829-462D-A98F-3CC27AE52E01_1_preview.jpg]
Best Wishes, Shane
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Shane S