External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run freesurfer on a resampled T1w scan and it has come up with segmentation fault error at the stages of the atlas.
I was wondering if the resampled T1w scan has caused this error and this is the only difference between processing before. I am really stuck and its not a system compatability issue as I have been able to run all of my freesurfer output without error before so anything would be great.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Performed on MobaXterm on windows computer using eddie super computer and Edinburgh university 3) uname -a: Linux node1c08.ecdf.ed.ac.uk 5.14.0-427.33.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Aug 28 17:34:59 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
Not sure if the above is fully correct. Any help would be greatly appreciated!
Best wishes
Samantha Hendry The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
I don't think resampling should have caused this error. Can you look at the aparc? Eg, cd $SUBJECTS_DIR/FMS_0094 tksurferfv FMS_0094 lh inflated -aparc -label labe/lh.cortex.label The cortex label will appear as bright yellow. Make sure it look ok, meaning everything covered except the non-cortical portions of the medial wall Then remove the label so that you can see the aparc. It should cover all the same parts as the label. You can also just look at the surfaces to make sure they are ok, eg, tkmeditfv FMS_0094 nu.mgz -surfs Does it happen for all your subjects or just this one?
On 7/25/2025 2:40 PM, Samantha Hendry wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run freesurfer on a resampled T1w scan and it has come up with segmentation fault error at the stages of the atlas.
I was wondering if the resampled T1w scan has caused this error and this is the only difference between processing before. I am really stuck and its not a system compatability issue as I have been able to run all of my freesurfer output without error before so anything would be great.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
- FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
- Platform: Performed on MobaXterm on windows computer using eddie
super computer and Edinburgh university
- uname -a: Linux node1c08.ecdf.ed.ac.uk 5.14.0-427.33.1.el9_4.x86_64
#1 SMP PREEMPT_DYNAMIC Wed Aug 28 17:34:59 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
- recon-all.log: see attached
Not sure if the above is fully correct. Any help would be greatly appreciated!
Best wishes
Samantha Hendry
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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...
External Email - Use Caution
Hi Douglas,
Thank you for your reply this only happens to a group of subjects from a certain site. Majority of cases have ran completely fine never encountered this error before.
The surfaces actually look alright I would say there is slight deviations from the GM for example not fully following the outline properly but its not extensive.
This is why I thought the output was good until I looked in the labels folder where there was only 4 files generated.
Any other ideas or things I could try would be greatly appreciated.
Best wishes
Samantha Hendry
From: Douglas N. Greve dgreve@mgh.harvard.edu Sent: 31 July 2025 14:33 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer labels not generated and have some corrupted label files
I don't think resampling should have caused this error. Can you look at the aparc? Eg, cd $SUBJECTS_DIR/FMS_0094 tksurferfv FMS_0094 lh inflated -aparc -label labe/lh.cortex.label The cortex label will appear as bright yellow. Make sure it look ok, meaning everything covered except the non-cortical portions of the medial wall Then remove the label so that you can see the aparc. It should cover all the same parts as the label. You can also just look at the surfaces to make sure they are ok, eg, tkmeditfv FMS_0094 nu.mgz -surfs Does it happen for all your subjects or just this one? On 7/25/2025 2:40 PM, Samantha Hendry wrote:
External Email - Use Caution Hello FreeSurfer Developers,
I'm attempting to run freesurfer on a resampled T1w scan and it has come up with segmentation fault error at the stages of the atlas.
I was wondering if the resampled T1w scan has caused this error and this is the only difference between processing before. I am really stuck and its not a system compatability issue as I have been able to run all of my freesurfer output without error before so anything would be great.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Performed on MobaXterm on windows computer using eddie super computer and Edinburgh university 3) uname -a: Linux node1c08.ecdf.ed.ac.uk 5.14.0-427.33.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Aug 28 17:34:59 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
Not sure if the above is fully correct. Any help would be greatly appreciated!
Best wishes
Samantha Hendry The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1Flpz46KqxGMrj_KwqljwT8i92n0UrWY6oezYoathus32OL...
External Email - Use Caution
Hi Douglas,
I will be leaving my job and wondering if possible to leave you with my colleague Rozanna (cc in this email) to continue this issue further.
I have appreciated the time you have taken to email and hope you have had a great day!
Best wishes
Samantha
From: Samantha Hendry shendry2@ed.ac.uk Sent: 04 August 2025 17:44 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer labels not generated and have some corrupted label files
External Email - Use Caution Hi Douglas,
Thank you for your reply this only happens to a group of subjects from a certain site. Majority of cases have ran completely fine never encountered this error before.
The surfaces actually look alright I would say there is slight deviations from the GM for example not fully following the outline properly but its not extensive.
This is why I thought the output was good until I looked in the labels folder where there was only 4 files generated.
Any other ideas or things I could try would be greatly appreciated.
Best wishes
Samantha Hendry
From: Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: 31 July 2025 14:33 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer labels not generated and have some corrupted label files
I don't think resampling should have caused this error. Can you look at the aparc? Eg, cd $SUBJECTS_DIR/FMS_0094 tksurferfv FMS_0094 lh inflated -aparc -label labe/lh.cortex.label The cortex label will appear as bright yellow. Make sure it look ok, meaning everything covered except the non-cortical portions of the medial wall Then remove the label so that you can see the aparc. It should cover all the same parts as the label. You can also just look at the surfaces to make sure they are ok, eg, tkmeditfv FMS_0094 nu.mgz -surfs Does it happen for all your subjects or just this one? On 7/25/2025 2:40 PM, Samantha Hendry wrote:
External Email - Use Caution Hello FreeSurfer Developers,
I'm attempting to run freesurfer on a resampled T1w scan and it has come up with segmentation fault error at the stages of the atlas.
I was wondering if the resampled T1w scan has caused this error and this is the only difference between processing before. I am really stuck and its not a system compatability issue as I have been able to run all of my freesurfer output without error before so anything would be great.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Performed on MobaXterm on windows computer using eddie super computer and Edinburgh university 3) uname -a: Linux node1c08.ecdf.ed.ac.uk 5.14.0-427.33.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Aug 28 17:34:59 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
Not sure if the above is fully correct. Any help would be greatly appreciated!
Best wishes
Samantha Hendry The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1mwjfRxRY3TwtIrz_aDj45YBEJ3EMwpABpK21l5Wd8UHTi8...https://secure-web.cisco.com/1Flpz46KqxGMrj_KwqljwT8i92n0UrWY6oezYoathus32OLwiL2wADFpax-IyYQgKFZEbGWCnIllt12svnd_7jU3ANA5b26P-YxaqiNsPsHyOh85QRWPMvP_mKQS8aExw_o9dSRP0lOLeqnWiJu0ty2aUhH7ku7NTEJfxbD7hAa_A7eBdwdBx_6VzNcBioORxmDF8J-YXelrORikiojyMwLaQo_H7O6E02fRH7IQbZ1kGUyGUZReHxypPEuHWEcx1uLmCMzL8H0LubpWdRmPrECosXCiFl5eKzdTltt6ZOCJRMgyEaEjoxP8az7BeqLeyUrsePs-Md4z9HOsVXqVJiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Samantha Hendry