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