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Hello FreeSurfer Support Team,

Sorry to jump into this thread, but I’ve been experiencing the same issue that Felix reported. My manual edits on wm.mgz resulted in identical surface outputs after rerunning recon-all -autorecon2-wm -autorecon3. I’ve tried removing the nu.mgz file as well as rerunning with the -all flag as you previously suggested, but the surfaces don’t appear to change.

I was wondering if there have been any updates on this, or if anyone has suggestions for how I can resolve it?

Thank you very much!

All the best,

Tiantian

From: Zahnert, Felix <fzahnert@mgh.harvard.edu>
Sent: Thursday, October 9, 2025 11:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged [EXTERNAL]

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Dear Douglas,

Thank you for your reply!

I just did. The surface did change by a tiny bit, but by far not as delineated in wm.mgz (same for non-lesional regions where wm simply extends into cortex).

Could it be that the surface generation does not strictly adhere to delineated wm.mgz, but still also considers the nu.mgz voxels in these respective regions? Could the intensities in my images just be too off?

I work at the Martinos in case you think it might be helpful to take a look- I could, for example, point you to the data on the server (not publicly of course.. ).

Thanks again!

Best,

Felix

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, October 9, 2025 9:03 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged

Hmmm, that should have done something. Can you try rerunning it using -all (instead of -autorecon...)? No harm in that, it just reruns processes that don't necessarily need to be rerun.

On 9/29/2025 6:52 PM, Zahnert, Felix wrote:

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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