Hi Bronwyn
Hard to say without seeing the data, but I would guess that there are topological defects causing these issues. You can overlay the locations of the defects in freeview and see if that explains things.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bronwyn Overs Sent: Friday, October 11, 2024 1:31 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill
External Email - Use Caution Dear Freesurfer Support,
I'm reviewing a specific MRI image that I have processed with Freesurfer V5.3. I'm concerned about a potential issue with voxels missing from the WM surface. This appears to impacting the pial boundaries and lateral ventricle labels in the aseg from slices 56-99. For reference, I attached 5 images (both wm and brainmask surfaces) that are each 5 slices apart. Happy to upload the whole series of images if this would be helpful.
Would you recommend filling in some of the voxels near the lateral ventricles? My concern is that I am unsure where the ventricle begins, as I suspect the gyrus at the rh pericalcarine surface is not being properly labelled and identified in the pial surface. Any advice you can provide will be greatly appreciated.
Kind regards,
Bronwyn Overs
Senior Research Assistant [cid:image001.png@01DB1BC1.D28744C0]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
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