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:

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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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