External Email - Use Caution
This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault. I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though. https://secure-web.cisco.com/17sKLSeDVET5-5S3ZEgRGL6lX55gFUMqV2UWISNObj-rC9p... But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5. - R. On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2@ed.ac.uk> wrote:mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white
External Email - Use Caution
Hi,
That’s is great thank you I will check it out sorry I think I gave you the wrong scripts here is a different one from this year fi this would make anymore sense thankyou! 😊
Best wishes
Samantha
From: fsbuild fsbuild@contbay.com Sent: 10 July 2025 22:16 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
External Email - Use Caution
This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault. I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though.
https://secure-web.cisco.com/1kII4TbCI49cZwwlOnHYFCUUaBglX8r7MQeqWDAa8DZ2GU4...
But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5.
- R.
On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> wrote:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white
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.
It looks like you ran into system compatibility issues. Your recon-all.log shows that you are running centos6 release on Linux 9 machine. See this thread for related discussions https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74552.html
Yujing
From: Samantha Hendry shendry2@ed.ac.uk Sent: Friday, July 11, 2025 1:54 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
External Email - Use Caution Hi,
That’s is great thank you I will check it out sorry I think I gave you the wrong scripts here is a different one from this year fi this would make anymore sense thankyou! 😊
Best wishes
Samantha
From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 10 July 2025 22:16 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
External Email - Use Caution
This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault. I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10245.htmlhttps://secure-web.cisco.com/1kII4TbCI49cZwwlOnHYFCUUaBglX8r7MQeqWDAa8DZ2GU4lEmYKOj_wbneyDbhaMjrSuD55XqcKpCtU_iuqlsEO_2fEr5F6Tu41whj0LnOvCI19zUC-wKVfcUxLuFs--dCTtM522Sdifs5dPqGb8Wx82Cc36u-16hr9ywCoylr26iyEQZp3nw0TzaoQ3beB_LZ7iOtWUE6KiGlFTpHnzymOvDt7sI02XGGpxixQ1k2jbYhR4Ef8hoyA-oxeYL38TDbLIqBA8aQz6rdwLChdsEvVJUKnCKI7h39V_5pBnimewrmf9JJZiAC3pU4h-xQKlS5HnXdYsny9sqYdnPCpsQA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg10245.html
But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5.
- R.
On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> wrote:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white
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.
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Hi,
Okay that is great thank you I will check it out but I have been able to run free surfer fab for a lot of subject data so I wondered if the resampled t2 had anything to do with this as I was able to run it before. Do you think it would still be a compatibility issue?
Best wishes
Samantha
From: Huang, Yujing YHUANG43@mgh.harvard.edu Sent: 14 July 2025 16:15 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
You don't often get email from yhuang43@mgh.harvard.edumailto:yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1jGVgy-jXIHqrI3SRUuuY3Juj8bumkh7buVnyzHXW9XVcX6xB-Hgc98DflZl5FPfq-B4CkJWjNcFupVG-Lv9_PGxWjFNb1KyZ0AfAR0Brn2z3bFnTVe3z_g___waAaLYel0yVj3KHh9qoL9Wpan2P20GtC2N3XJ4xrUVrDQji0sDWP1xktw9IO6zXX3iuODWcIRRVZfXJw9stbtj3hCcqlcAX37ptbobMw9zEpthDOlaIbaRGNK5EaF4ZicNKMgENeo_PzSSqhJnILTA04JRmprwdLA5arCX-CiXOJNZtfpaz4-fX1jZKqvtbAHLY3yxH/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification It looks like you ran into system compatibility issues. Your recon-all.log shows that you are running centos6 release on Linux 9 machine. See this thread for related discussions https://secure-web.cisco.com/1Kj5_s8h5d3dNnzPC13-H0q5J7WwAcNqNQiF3lbpSoscvqy...
Yujing
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: Friday, July 11, 2025 1:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
External Email - Use Caution Hi,
That’s is great thank you I will check it out sorry I think I gave you the wrong scripts here is a different one from this year fi this would make anymore sense thankyou! 😊
Best wishes
Samantha
From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 10 July 2025 22:16 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
External Email - Use Caution
This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault. I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though.
https://secure-web.cisco.com/1D_dnijHOMxYhHbRv4HNQ8w1ig2P4sAJcBSV9WQRzaO1sHy...https://secure-web.cisco.com/1kII4TbCI49cZwwlOnHYFCUUaBglX8r7MQeqWDAa8DZ2GU4lEmYKOj_wbneyDbhaMjrSuD55XqcKpCtU_iuqlsEO_2fEr5F6Tu41whj0LnOvCI19zUC-wKVfcUxLuFs--dCTtM522Sdifs5dPqGb8Wx82Cc36u-16hr9ywCoylr26iyEQZp3nw0TzaoQ3beB_LZ7iOtWUE6KiGlFTpHnzymOvDt7sI02XGGpxixQ1k2jbYhR4Ef8hoyA-oxeYL38TDbLIqBA8aQz6rdwLChdsEvVJUKnCKI7h39V_5pBnimewrmf9JJZiAC3pU4h-xQKlS5HnXdYsny9sqYdnPCpsQA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg10245.html
But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5.
- R.
On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> wrote:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white
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@nmr.mgh.harvard.edu
-
fsbuild -
Huang, Yujing -
Samantha Hendry