The problem here is that the white surface is not extending far enough
because the white matter is underlabeled. I know it seems intuitive to
edit the aseg to influence the the surface placement, it actually will
have very little effect. In this case, you should edit the wm.mgz to
fill in the WM in that area then run recon-all -s subject -autorecon2-wm
-autorecon3
On 5/21/2022 7:25 AM, Helena Pereira wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to get the new surface pial from the grey-matter. I
note that the grey-matter from the temporal areas is not correctly
segmented (a few slices are not identified as grey-matter nor with any
label) in the aseg file, which influences the surface pial of the grey
matter. To correct this, I manually corrected the aseg file expecting
to get the correct surface pials. Nevertheless, after running
recon-all make -all, the surface remains the same.
I've searched the list and no similar errors have been reported. Does
anyone have any thoughts on how to trouble-shoot this one?
Also, I've attached an example of my problem, after recon-all make -all.
1) FreeSurfer version: 7.1.1
2) Operating system info: AlmaLinux 8.5, rhel centos fedora 8.5
Thanks in advance,
Best regards,
Helena Pereira
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