Hi Renat,

The third defect is too large and it’s causing a crash. When I run it, it hangs forever at:

CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash.

There are huge gaps missing in this subject’s white matter mask, resulting in a bad surface tessellation (see attached pic). I would check out the info at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... and fill in the wm.mgz to manually edit.

best Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yakupov, Renat /DZNE Renat.Yakupov@dzne.de Date: Thursday, May 6, 2021 at 4:21 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Hi Andrew,

thank you for your reply. I just uploaded the subject's directory under the name "subject_from_RenatYakupov.tar.gz".

Regarding memory, I am running these jobs on our SGE cluster, which monitors memory usage. Both of the subject's images had maximum memory usage of slightly over 3GB, which is pretty typical from my experience. Interestingly, when processed with Freesurfer 6, which didnt crash and finished successfully, the maximum memory usage was around 11GB.

Thanks again and looking forward to your findings 😊

Best wishes, Renat. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@MGH.HARVARD.EDU Sent: Wednesday, May 5, 2021 7:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

Hi Renat,

That 3rd defect is fairly large – normally it would hang but it’s possible you’re running out of memory. If you can zip the subject and file drop it to us, we can take a look:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchangehttps://secure-web.cisco.com/1u2I9K-ckbULcDN4h-_ZdylX5n2vBBOMX6EHfWnDs7-xWZI3mqQdWi7HFoMKz9tdNYKjuWfN_Nan4JpJGREsnwmGq3yxwMImknbbPMfasAVeeqV3mWyJDJQbZi7QtsM0L44JYsK6UYk_wuuwEf_p_Ed5vbQFvnR_qkoiA75YR3ueRivLu1VsrmbDCfIglg4xLUeLcU3w4JopYBtaAk1pJe5CQJ-Nwjy6wxShFB-45MwaCw2xP54Ka9a36Silz4XoVQFam74VwOrlnybPLjm3TGQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange

best,

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yakupov, Renat /DZNE Renat.Yakupov@dzne.de Date: Friday, April 30, 2021 at 11:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Dear all,

I have a subject whose Freesurfer processing crashes during topology fixing step. The last lines in `recon-all.log` are:

After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157) : difference with theory (-18) = -3 CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369) Segmentation fault (core dumped) Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST 2021

For the full `recon-all.log` and `recon-all.error` files please see the attached files.

I tried to follow the manual topology fixing instructions from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...https://secure-web.cisco.com/1CVb3gwDr9GTwil5kr7FQYCZpGmZhLu9ovxhkC6nEa1QhFJIx6eypmT0rYaI6M3eFoajm5UGJThFtpEwrTovzNAg_qegvhWDxcy-m6gpWYAx55QHi7-eJxrS108DfdnILY9yauaca2pTGvSgA9CrUOR9Twoqnu5o6E2uJ_bMuvqjHfdZuxVU9dNQ0n1Pi4WCFH3_4H6PQilZLYZai-fJAGrNEqr7pFG9jzwrssq82FVnCamJT0vmbbW9I27W_DE1vKkW9T7lo9aEi6hbNTu3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview, but *.white and *.pial surface files are missing from `surf` directory. It only contains these files:

lh.defect_borders lh.defect_labels lh.orig.nofix lh.smoothwm.nofix rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.qsphere.nofix rh.inflated.nofix rh.qsphere.nofix

Which files can I use in place of white and pial surface files in order to look for WM segmentation defects?

Some additional information about the data:

- I am running Freesurfer 7.1

- overall, there are no gross errors in WM segmentation, although the subjects does have significant temporal lobe atrophy

- there are two images acquired at different times, and processing fails for both images

- interestingly, processing didnt crash with Freesurfer 6.

Thank you and have a great weekend,

Renat.

Yes, it might be a normalization issue. You could try using the `-no-ants-n4` recon-all flag to fallback to the v6 normalization method.

As for the wm edits, you don’t really need to load the surfaces, just the norm.mgz and wm.mgz, but if you wanted to visualize the initial smooth tessellation as well:

freeview -v mri/norm.mgz mri/wm.mgz:colormap=heat:opacity=0.5 -f surf/?h.smoothwm.nofix

best Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yakupov, Renat /DZNE Renat.Yakupov@dzne.de Date: Friday, May 7, 2021 at 6:00 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Hi Andrew,

thank you for looking at the data!

I did check out that tutorial first, and the first thing it tells you to do is load various surfaces into Freeview, which was what brought me here. In this subject's `surf` directory there are no ?h.white and ?h.pial surface files. Which files can I use instead in order to see the white matter surface and look for those defects?

It is also interesting, that the processing didnt fail in Freesurfer 6. Looking at the release notes, one of the changes was using N4 bias-field correction instead of N3. Do you think this might mean that N4's inadequate bias-field correction led to broken-up segmented white matter, which in turn caused larger topological defects?

Best wishes,

Renat.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@MGH.HARVARD.EDU Sent: Friday, May 7, 2021 5:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

Hi Renat,

The third defect is too large and it’s causing a crash. When I run it, it hangs forever at:

CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369)

An extra large defect has been detected...

This often happens because cerebellum or dura has not been removed from wm.mgz.

This may cause recon-all to run very slowly or crash.

There are huge gaps missing in this subject’s white matter mask, resulting in a bad surface tessellation (see attached pic). I would check out the info at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...https://secure-web.cisco.com/12gT4H7XBsnxMWWCG4F8T4qJBE2PnbITfcdxpaBTxDgzaZPjHt1Catp497o4oUcQVkGOLdV1H5oPZEhAnsBEWow0_4VGH6FsatlW_uUq3bBc-hRCpHluu5XhEuB-KQOMYmA6arEafPIf63cVVzOyZIn4hG1sVKMtcFUPlyUovEhCmOtR0jOZIyYiy7FQeC2_hSbRngcTvJKSaaE9nCnXO2Law1dP6lPrceor8a4XTA3T_mew60k5qF8QD5Vmg2YWpbOhlp1IWt2BeJQ0sfT1yQQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview and fill in the wm.mgz to manually edit.

best

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yakupov, Renat /DZNE Renat.Yakupov@dzne.de Date: Thursday, May 6, 2021 at 4:21 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Hi Andrew,

thank you for your reply. I just uploaded the subject's directory under the name "subject_from_RenatYakupov.tar.gz".

Regarding memory, I am running these jobs on our SGE cluster, which monitors memory usage. Both of the subject's images had maximum memory usage of slightly over 3GB, which is pretty typical from my experience. Interestingly, when processed with Freesurfer 6, which didnt crash and finished successfully, the maximum memory usage was around 11GB.

Thanks again and looking forward to your findings 😊

Best wishes,

Renat.

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@MGH.HARVARD.EDU Sent: Wednesday, May 5, 2021 7:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

Hi Renat,

That 3rd defect is fairly large – normally it would hang but it’s possible you’re running out of memory. If you can zip the subject and file drop it to us, we can take a look:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchangehttps://secure-web.cisco.com/1u2I9K-ckbULcDN4h-_ZdylX5n2vBBOMX6EHfWnDs7-xWZI3mqQdWi7HFoMKz9tdNYKjuWfN_Nan4JpJGREsnwmGq3yxwMImknbbPMfasAVeeqV3mWyJDJQbZi7QtsM0L44JYsK6UYk_wuuwEf_p_Ed5vbQFvnR_qkoiA75YR3ueRivLu1VsrmbDCfIglg4xLUeLcU3w4JopYBtaAk1pJe5CQJ-Nwjy6wxShFB-45MwaCw2xP54Ka9a36Silz4XoVQFam74VwOrlnybPLjm3TGQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange

best,

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yakupov, Renat /DZNE Renat.Yakupov@dzne.de Date: Friday, April 30, 2021 at 11:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Dear all,

I have a subject whose Freesurfer processing crashes during topology fixing step. The last lines in `recon-all.log` are:

After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157) : difference with theory (-18) = -3 CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369) Segmentation fault (core dumped) Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST 2021

For the full `recon-all.log` and `recon-all.error` files please see the attached files.

I tried to follow the manual topology fixing instructions from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...https://secure-web.cisco.com/1CVb3gwDr9GTwil5kr7FQYCZpGmZhLu9ovxhkC6nEa1QhFJIx6eypmT0rYaI6M3eFoajm5UGJThFtpEwrTovzNAg_qegvhWDxcy-m6gpWYAx55QHi7-eJxrS108DfdnILY9yauaca2pTGvSgA9CrUOR9Twoqnu5o6E2uJ_bMuvqjHfdZuxVU9dNQ0n1Pi4WCFH3_4H6PQilZLYZai-fJAGrNEqr7pFG9jzwrssq82FVnCamJT0vmbbW9I27W_DE1vKkW9T7lo9aEi6hbNTu3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview, but *.white and *.pial surface files are missing from `surf` directory. It only contains these files:

lh.defect_borders lh.defect_labels lh.orig.nofix lh.smoothwm.nofix rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.qsphere.nofix rh.inflated.nofix rh.qsphere.nofix

Which files can I use in place of white and pial surface files in order to look for WM segmentation defects?

Some additional information about the data:

- I am running Freesurfer 7.1

- overall, there are no gross errors in WM segmentation, although the subjects does have significant temporal lobe atrophy

- there are two images acquired at different times, and processing fails for both images

- interestingly, processing didnt crash with Freesurfer 6.

Thank you and have a great weekend,

Renat.