10 Aug
2025
10 Aug
'25
6:25 p.m.
I would not exclude the case. I would probably leave it as is if the rest of the brain looks ok. The problem is that the skull stripping is not removing that very bright area next to cortex. If you wanto fix it, then edit brain.finalsurfs.manedit.mgz to remove the voxels. btw, I don't think that is dura. Rather, you probably have a low-bandwidth scan and the fat is shifting near cortex.
On 7/31/2025 3:00 PM, Mahta Abbaspour wrote:
External Email - Use Caution
Thank you. I just wanted to clarify a bit. The images I sent earlier in my previous email were actually mild cases of incorrect filled.mgz. I’d like you to take a look at one of the more recent scans I worked on.
image.png The first slice is from before I edited the filled.mgz. There were some dura voxels that had been misclassified as white matter, so I removed them, expecting the WM and pial surfaces to fix automatically. image.png In the second slice (same slice after the edit), you can see that both the filled.mgz and WM surface look better, but the pial surface is still picking up some dura in that same spot. This happens consistently across slices where I cleaned up the misclassified voxels in fille.mgz mask. Also, on the right side of the image (which looked fine before), the pial surface is now grabbing dura after the edit.
So my question is if the filled.mgz and WM surface look fine after editing but the pial surface still picks up dura, should I just leave it as is? Or is this a case where I should consider excluding these scans altogether?
Best, Mahta
On Thu, 31 Jul 2025 at 09:27, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
For the last image, it is hard to say without a before and after picture. That area you point to looks like the filled extends too far, but the white surface might be ok. The white surface is often jagged in this location because it is highly myelinated and the boundaries are not clear. The pial surface does not look that bad. It is grabbing a little bit of dura. I would probably leave it the way it is. I think you are probably editing too much, trying to track down every little place where the pial grabs dura. There are going to be a lot of them, and it is not clear that fixing them will really help your downstream analysis On 7/25/2025 1:15 PM, Mahta Abbaspour wrote:External Email - Use Caution You're right. The filled.mgz mask did include non-white matter voxels. I removed those and regenerated the surface. While that fixed the issue in those particular slices, it caused new problems in the following slices that were previously fine. Please see below. image.png This was the filled.mgz masks before manual intervention. image.png This is after removing those non-wm voxels in dura (same slice as top). image.png image.png Here are a few slices following the previous one. As you can see, the filled.mgz looks accurate, but the wm surface placement is now off. It also seems like the wm surface has become jagged. Additionally, the pial surface now extends into the dura in these slices, which wasn’t an issue before. At this point, I’m a bit stuck. I've already tried several manual interventions to fix this common issue in my dataset. I’d really appreciate any feedback or insight you might have. Thank you. On Wed, 23 Jul 2025 at 09:20, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: It is probably the case that the bright spot is being misclassified as WM. For that error, the fix is to edit the filled.mgz (from which the white surface is constructed). Once the white surface is fixed, the pial may look ok. On 7/22/2025 11:50 AM, Mahta Abbaspour wrote:External Email - Use Caution 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. image.png 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: image.png 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/ 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:External Email - Use Caution 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:External Email - Use Caution 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? image.png image (1).png - 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. image (2).png 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:External Email - Use Caution 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:> > External Email - Use Caution > > 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. > > image.png > > > _______________________________________________ > Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu > To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e... https://secure-web.cisco.com/1cHvwKFmJYPumH8G-nguANqIqTXcIj2S1t4QcBn3uR9AhhI3SHxdXcTGQuqqNB7ArERv-cX9LXrDUcciTgV4CxG8E11q0gyn1S6t5bhUBO5eY5Z0d5dXRt8ZP--m47jAOeif_7PI2Ox_GEG7ZnhVqbmfKhND1IWv9KL6RrgmS-J5trtrFhDoWLjxmG76FGjd_jpmunt4zAuf9dEoFPFOhEBHo60y1GKa-5kIvEeXICuqFrtb280szKDPLgCnicBKU7co_ws0grwYRlSaQTOX2vkQ1mJ6GgSkC7Adk2rETv3QffB0B9AeISz8WlMAO8c9kA8tNfm--MdESfX-q-lPJ2w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F
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