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Hi. No, in the screenshot I sent the pial was not extending to dura and surfaces look accurate. My followup question is that even though it did not mess up the surface, should I still think about editing it? because any inclusion of non-brain tissue especially across a large number of slices would affect total intracranial volume, right?

On Sun, 20 Jul 2025 at 18:40, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Are you saying that the pial surface is extending into the dura? If so, can you zoom in and highlight? The surfaces look ok in the the slice that you show. 

On 7/14/2025 3:12 PM, Mahta Abbaspour wrote:

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I forgot to mention that I’m using v8.

On Mon, Jul 14, 2025 at 1:32 PM Mahta Abbaspour <mahtaabbaspour96@gmail.com> wrote:
Hello Freesurfer team,

I'm currently performing QC on the FreeSurfer outputs and noticed that in many scans, there’s consistent inclusion of dura near the occipital lobe and cerebellum, spanning approximately 10–40 slices sometimes. No dura is included in the anterior or middle slices.
I had two questions:
  • Do you have any idea why this might be happening? The pial and white matter surfaces look fine throughout.
  • What would be the best way to address this? Should I manually remove the dura and regenerate the surfaces — though this is quite labor-intensive, especially when it affects many slices — or should I consider adjusting the -h parameter for more aggressive skull stripping? However, brainmask also look fine in all other regions.

I’ve attached a screenshot from one of the slices for reference. I’d appreciate any suggestions you might have. Thank you.

image.png

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