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
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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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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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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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.edumailto:dgreve@mgh.harvard.edu Sent: Sunday, September 28, 2025 10:50 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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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]
* External Email - Caution *
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.edumailto:dgreve@mgh.harvard.edu Sent: Sunday, September 28, 2025 10:50 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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Hi Tiantian, I'm using a 'hack' to circumvent this issue now, which kind of works but is perhaps not optimal.
* After the manual wm edits, I run autoreon2-wm (perhaps not necessary, since changes are not used by fs?) * Recon edit results in edited voxels in wm.mgz to appear as 1 (deleted) or 255 (added; I rarely did this and only in lesional areas- adding controlpoints works just fine) * I create a copy of brain.finalsurfs.mgz (just as backup); then, I create a mask of all wm.mgz voxels that are == 1 and I set the same voxels in brain.finalsurfs.mgz to a value of 60 (arbitrary, but like gm). Wm.mgz Voxels == 255 are set to 255 in brain.finalsurfs.mgz. * When just running recon-all -s <subject> -autorecon3 afterwards, the changes appear on the wm surface.
However, I'm curious, too, if there is a better solution than this. Best, Felix ________________________________ From: Lei, Tiantian Tiantian.Lei@childrens.harvard.edu Sent: Tuesday, December 2, 2025 5:28 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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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]
* External Email - Caution *
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.edumailto:dgreve@mgh.harvard.edu Sent: Sunday, September 28, 2025 10:50 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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have tried editing the filled.mgz instead of wm.mgz? In the end, it should not matter, but the editing in recon-all is a bit complicated and we edit the filled.mgz. You can also try 8.1 as it will give the same output when not-editing.
On 12/3/2025 10:57 AM, Zahnert, Felix wrote:
Hi Tiantian, I'm using a 'hack' to circumvent this issue now, which kind of works but is perhaps not optimal.
- After the manual wm edits, I run autoreon2-wm (perhaps not necessary, since changes are not used by fs?)
- Recon edit results in edited voxels in wm.mgz to appear as 1 (deleted) or 255 (added; I rarely did this and only in lesional areas- adding controlpoints works just fine)
- I create a copy of brain.finalsurfs.mgz (just as backup); then, I create a mask of all wm.mgz voxels that are == 1 and I set the same voxels in brain.finalsurfs.mgz to a value of 60 (arbitrary, but like gm). Wm.mgz Voxels == 255 are set to 255 in brain.finalsurfs.mgz.
- When just running /recon-all -s <subject> -autorecon3 /afterwards, the changes appear on the wm surface.
However, I'm curious, too, if there is a better solution than this. Best, Felix
*From:* Lei, Tiantian Tiantian.Lei@childrens.harvard.edu *Sent:* Tuesday, December 2, 2025 5:28 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Re: wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged [EXTERNAL]
External Email - Use Caution
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] ** External Email - Caution **
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 mailto:dgreve@mgh.harvard.edu *Sent:* Sunday, September 28, 2025 10:50 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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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Douglas N. Greve -
Lei, Tiantian -
Zahnert, Felix