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Hi Bruce,
Thanks for your answer. I have checked the wm.mgz but it does not seem to be a topological error I think. I have added coronal, axial, and sag views in attachment (see the red cursor). Also I have added the first (coronal) slice that starts to show white matter (couple slices later).
Let me know if you still would like me to upload the data.
Best Julie
On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Julie
It’s hard to tell from the single slice. Is there white matter in the wm.mgz that doesn’t have surface (?h.white) covering it? That would indicate a topological defect.
If you upload the entire gzipped and tarred subject’s directory we will take a look
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy *Sent:* Sunday, October 11, 2020 3:51 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Fixing error with pial surface
External Email - Use Caution *Dear Freesurfer team,
I have a question related to fixing the pial surface when a part was missed (see attachment). On the freesurfer website, I only found how to erase the pial when there was too much (see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I could not find what to do when there was too little.
As there is no white matter in this particular area, it is also not an option to place control points. Also the skull stripping did not change anything: I tried both the freesurfer skull stripping and an in-house skull stripping algorithm.
Thank you for your help.
Best regards
Julie
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