Hi Felix, this might be a result of an error in 8.0 (sorry). Try using 8.1 instead. You can run it the same folder (and keep your edits), but before you do, delete the nu.mgz file. Hopefully this will solve your problem.

On 9/26/2025 1:14 PM, Zahnert, Felix wrote:

Dear experts,

I have run recon-all using Freesurfer 8.0.0 and corrected wm.mgz in some subjects (deleting voxels where ?h.white grossly extended into gm by assigning them values of 1; adding voxels where juxtacortical hypointensities were misclassified as gm by assigning them 255).

After these edits (and saving wm.mgz), I ran recon-all -s <subject> -autorecon2-wm -autorecon3.

However, this left the reconstructed surfaces virtually unchanged. Even areas of larger edits are left unchanged. I did check for small areas of stray voxels that could have led to such misclassification.

In the documentation, it is recommended to run recon-all with the -make flag in such cases, which no longer seem to be supported.

Do you have any recommendations?

Thank you so much,

Best,

Felix
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