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Got it—I'll ignore those cases then. Thanks again
for taking the time to answer my questions. I have one more
follow-up.
While QC the output, I’ve come across some more severe cases where manual edits to the pial surface seem necessary. In some instances, the pial surface extends into the dura, which leads to misplacement of both the pial and sometimes the wm surface. I’ve attached an example below—take a look at the top left edge.
I’m not quite sure why this keeps happening—lowering the -h value doesn’t seem to help (I've also tried -h=15). In fact, it makes the surface reconstruction worse by introducing errors in new areas. I’d really appreciate any insights you might have on this!
While QC the output, I’ve come across some more severe cases where manual edits to the pial surface seem necessary. In some instances, the pial surface extends into the dura, which leads to misplacement of both the pial and sometimes the wm surface. I’ve attached an example below—take a look at the top left edge.
For this subject, I manually removed dura from the
brainmask twice and regenerated the surface, but each time,
things got even messier and the results didn’t improve. So, I
decided to adjust the watershed threshold by lowering the -h
value to 20. Please see the updated result from the same slice
below:
Not only did skull stripping not improve, but I also
noticed that the pial surface extended into regions that were
previously unaffected.
Here's the command I used:
recon-all -skullstrip -wsthresh 20 -clean-bm -s
PVS_2_005
recon-all -autorecon-pial -s PVS_2_005
recon-all -autorecon-pial -s PVS_2_005
I’m not quite sure why this keeps happening—lowering the -h value doesn’t seem to help (I've also tried -h=15). In fact, it makes the surface reconstruction worse by introducing errors in new areas. I’d really appreciate any insights you might have on this!
Best,
Mahta
On Tue, 22 Jul 2025 at 09:23,
Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:
I see the extension of the pial surface into the dura in the figure on the left. In my opinion, the extension is so small that I would not bother trying to fix it. As you note, fixing that kind of thing can take lots of time. I don't think the error is worth the effort._______________________________________________
On 7/21/2025 12:14 PM, Mahta Abbaspour wrote:
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Thank you for the clarification. Could you also share your insights for my second question?
On Mon, Jul 21, 2025 at 11:48 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
right_______________________________________________
On 7/20/2025 10:37 PM, Mahta Abbaspour wrote:
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Thank you.
-Based on what you said, when the dura is included in the brain mask but it did not affect the pial and wm surface (please see 2 different scans below), we could ignore it, right?
- My followup question is that, there are scans in which inclusion of dura clearly causes the pial and wm surface to be distorted. For these types of errors, it's absolutely necessary to remove dura. I first tried manually removing dura across nearly 40-50 slices -which is not efficient at all- and regenerated the surface but it did not work as I expected. So that's when I thought about adjusting skull stripping parameters (I'm using v8). I tried adjusting the skull stripping parameters, including decreasing preflooding height (-h) to 15 and 20. Unfortunately, it messed up both pial and white matter surface placement and dura was only partially removed. I provided the illustration below. On the left, a subject's scan before skull stripping adjustment. You can see the pial surface was extended a bit to dura in superior lateral edges and across several slices. On the right, same subjects, after lowering the -h to 15 in skull stripping.
On Sun, 20 Jul 2025 at 22:28, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
No, the ICV is an *estimate* computed from the talairach transform. The existence of the dura plays no role. If you are using v8, you can get a segmentation-based ICV, and that would be affected if the dura is being segmented as cortex. Look at the aseg.presurf.mgz to see if this is happening. Even if it happens a little, I don't think it will affect much._______________________________________________
On 7/20/2025 7:05 PM, Mahta Abbaspour wrote:
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Hi. No, in the screenshot I sent the pial was not extending to dura and surfaces look accurate. My followup question is that even though it did not mess up the surface, should I still think about editing it? because any inclusion of non-brain tissue especially across a large number of slices would affect total intracranial volume, right?
On Sun, 20 Jul 2025 at 18:40, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Are you saying that the pial surface is extending into the dura? If so, can you zoom in and highlight? The surfaces look ok in the the slice that you show._______________________________________________
On 7/14/2025 3:12 PM, Mahta Abbaspour wrote:
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I forgot to mention that I’m using v8.
On Mon, Jul 14, 2025 at 1:32 PM Mahta Abbaspour <mahtaabbaspour96@gmail.com> wrote:
Hello Freesurfer team,
I'm currently performing QC on the FreeSurfer outputs and noticed that in many scans, there’s consistent inclusion of dura near the occipital lobe and cerebellum, spanning approximately 10–40 slices sometimes. No dura is included in the anterior or middle slices.
I had two questions:
- Do you have any idea why this might be happening? The pial and white matter surfaces look fine throughout.
- What would be the best way to address this? Should I manually remove the dura and regenerate the surfaces — though this is quite labor-intensive, especially when it affects many slices — or should I consider adjusting the -h parameter for more aggressive skull stripping? However, brainmask also look fine in all other regions.
I’ve attached a screenshot from one of the slices for reference. I’d appreciate any suggestions you might have. Thank you.
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