Dear Douglas, Thank you for your reply. Unfortunately, that did not work. I've removed nu.mgz and rerun 'recon-all -s <subject> -autorecon1' before running 'recon-all -s <subject> -autorecon2-wm -autorecon3', both using fs 8.1.0. Again, surfaces did not change. I reran it using fs7.4.1 just to check, which also did not substantially differ in areas of edits. I then set a ridiculous amount of wm.mgz to 1 using recon edit and reran recon-all in fs 8.1.0 as above, which also did not change results at all. Am I doing something wrong? Thank you! Best, Felix ________________________________ From: Douglas N. Greve dgreve@mgh.harvard.edu Sent: Sunday, September 28, 2025 10:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged
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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