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From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error. #@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz... reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial... reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 182364 Total vertex volume 180081 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Segmentation fault (core dumped) 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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2...
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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.
If it is possible for you to share the data, we can take a closer look.
Yujing
From: Samantha Hendry shendry2@ed.ac.uk Sent: Tuesday, July 29, 2025 10:51 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution
From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edumailto:analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error. #@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz... reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial... reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 182364 Total vertex volume 180081 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Segmentation fault (core dumped) 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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2o6-IjfHYfI6zvjsGMfsxmclfev49n6DBAZc9WmJaGOkLcq4cjaXnmD0CCNQ-JCGR5gTKPpSNvw4yPr5dxn8lzb0JNSpdKJ905rBHuuFW-9uC7nXx31Ez0dC1ssWO5_GKNDppLrocZxj8X_m8ZYMKjtUBhxUlh04pg3eLSzE0fPaWVPTGsvORq9066H1VwxiiCLntQDvnp8q5dXRsHHDEGRH5MQSODT2L5iXHL-R69v9oJrWwOT5lN8FbjWYNrGlRm7vYnFnzLZt47i054BuYxcwfc1Bu02A6OIdvC6g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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.
External Email - Use Caution
Hi,
Yes that would be great what data do you need? All of the freesurfer output?
Best wishes
Samantha Hendry
Sent from Outlook for iOShttps://secure-web.cisco.com/1jITrGlBfvVxv_MV1yz4EADQssdmzO311rvsBFFb032yWp3yzWbcfo3fO5qanYltZKMDVTK1sQUa9eh6-0o22sSRiZqopDJhx80831fai0gIVKJ7JNz-V0V4aqlJv74eydSZzlZLIlwDCIwxukcp8t02Pu_t0uj9kNR0ewvFItut6BE4i7Qcr_LTTdeOoKniMABNLkmnmA8bdfnUwJ-iMTDv2648sN6Ggw_M9W2zUuKCW3hUUHeCbbQCjfzV4EMQYnN4wFDIfMsYOJVctbsmpGb59sa6QErnSOPmcoJHPqew-MXEsO4tHAvPejZGpknQHec3lbnK5gZEd0LLQUpK3Qg/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Tuesday, July 29, 2025 4:48:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
You don't often get email from yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1mb91cgj0OgjO89KXOyVtnqCW9kORHeHJIj4RZbwY2fpls0MoJkYrOcSMvkgqBoL_6CHyZ8M6BBNHOln5BTNA5J44j8Fov5h-0UPARIP1Ucnc0Y6ADNv2Ck7c8VugzQyQM-LmYfPAWyG8GZ8SgSaYY1LEzlCEEB4h0OapgOCChYUKm8k8KtXqZsSiSo6TCyZjhruwFHWmxIDwqdEw-BoBpbc69PnPaJELUAkvap4rrlEbUGKgKo5nEguMjPLZ3w9PvBm3JZqwn8meORclmYnGQEyMZ0vBoy2LhpS4MRs2L0smP7pIq42BewZacHvMhjcQ2GGRY_hkeXZJmBBa82cB9g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
If it is possible for you to share the data, we can take a closer look.
Yujing
From: Samantha Hendry shendry2@ed.ac.uk Sent: Tuesday, July 29, 2025 10:51 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution
From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edumailto:analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error.
#@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025
/exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz...
reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial...
reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 182364
Total vertex volume 180081 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Segmentation fault (core dumped)
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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://secure-web.cisco.com/1r7-ds4MiAzZsYJZqRxR8FqKP0ZxkA_rC_Q0mO_vPSEK8rRW...http://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2o6-IjfHYfI6zvjsGMfsxmclfev49n6DBAZc9WmJaGOkLcq4cjaXnmD0CCNQ-JCGR5gTKPpSNvw4yPr5dxn8lzb0JNSpdKJ905rBHuuFW-9uC7nXx31Ez0dC1ssWO5_GKNDppLrocZxj8X_m8ZYMKjtUBhxUlh04pg3eLSzE0fPaWVPTGsvORq9066H1VwxiiCLntQDvnp8q5dXRsHHDEGRH5MQSODT2L5iXHL-R69v9oJrWwOT5lN8FbjWYNrGlRm7vYnFnzLZt47i054BuYxcwfc1Bu02A6OIdvC6g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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.
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Hi,
What would help to transfer specifically I am not sure how to send all of it?
Best wishes
Samantha
From: Samantha Hendry shendry2@ed.ac.uk Sent: 29 July 2025 18:40 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution Hi,
Yes that would be great what data do you need? All of the freesurfer output?
Best wishes
Samantha Hendry
Sent from Outlook for iOShttps://secure-web.cisco.com/1jITrGlBfvVxv_MV1yz4EADQssdmzO311rvsBFFb032yWp3yzWbcfo3fO5qanYltZKMDVTK1sQUa9eh6-0o22sSRiZqopDJhx80831fai0gIVKJ7JNz-V0V4aqlJv74eydSZzlZLIlwDCIwxukcp8t02Pu_t0uj9kNR0ewvFItut6BE4i7Qcr_LTTdeOoKniMABNLkmnmA8bdfnUwJ-iMTDv2648sN6Ggw_M9W2zUuKCW3hUUHeCbbQCjfzV4EMQYnN4wFDIfMsYOJVctbsmpGb59sa6QErnSOPmcoJHPqew-MXEsO4tHAvPejZGpknQHec3lbnK5gZEd0LLQUpK3Qg/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, July 29, 2025 4:48:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
You don't often get email from yhuang43@mgh.harvard.edumailto:yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1mb91cgj0OgjO89KXOyVtnqCW9kORHeHJIj4RZbwY2fpls0MoJkYrOcSMvkgqBoL_6CHyZ8M6BBNHOln5BTNA5J44j8Fov5h-0UPARIP1Ucnc0Y6ADNv2Ck7c8VugzQyQM-LmYfPAWyG8GZ8SgSaYY1LEzlCEEB4h0OapgOCChYUKm8k8KtXqZsSiSo6TCyZjhruwFHWmxIDwqdEw-BoBpbc69PnPaJELUAkvap4rrlEbUGKgKo5nEguMjPLZ3w9PvBm3JZqwn8meORclmYnGQEyMZ0vBoy2LhpS4MRs2L0smP7pIq42BewZacHvMhjcQ2GGRY_hkeXZJmBBa82cB9g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
If it is possible for you to share the data, we can take a closer look.
Yujing
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: Tuesday, July 29, 2025 10:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution
From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edumailto:analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error.
#@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025
/exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz...
reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial...
reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 182364
Total vertex volume 180081 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Segmentation fault (core dumped)
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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://secure-web.cisco.com/1JzfJ-nrlQhdLyP5WxfTIHwJA6NeSQaxMPu3xvy4M0oNrJNE...http://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2o6-IjfHYfI6zvjsGMfsxmclfev49n6DBAZc9WmJaGOkLcq4cjaXnmD0CCNQ-JCGR5gTKPpSNvw4yPr5dxn8lzb0JNSpdKJ905rBHuuFW-9uC7nXx31Ez0dC1ssWO5_GKNDppLrocZxj8X_m8ZYMKjtUBhxUlh04pg3eLSzE0fPaWVPTGsvORq9066H1VwxiiCLntQDvnp8q5dXRsHHDEGRH5MQSODT2L5iXHL-R69v9oJrWwOT5lN8FbjWYNrGlRm7vYnFnzLZt47i054BuYxcwfc1Bu02A6OIdvC6g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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.
You have sent two different recon-all.log. I noticed they were run on different machines.
The recon-all finished without errors was run on Linux7. The run failed with core dump was run on Linux9.
There are 3 runs in the recon-all.log with core dump errors: /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -i /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT1w.nii.gz -autorecon1 -noskullstrip /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -T2 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT2wreg2T1w.nii.gz -T2pial -autorecon2 -autorecon3 /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -T2 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT2wreg2T1w.nii.gz -T2pial -autorecon2-wm -autorecon3
'mris_anatomical_stats' core dumped for the 2nd and 3rd runs. 1st run finished without error but it didn't run mris_anatomical_stats'.
You are using FS6.0 built for centos6. It is possible the binaries are compatible with Linux7 but not Linux9. Before you send the files, can you try to run it on a Linux7 machine?
Yujing
From: Samantha Hendry shendry2@ed.ac.uk Sent: Tuesday, July 29, 2025 5:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution Hi,
What would help to transfer specifically I am not sure how to send all of it?
Best wishes
Samantha
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: 29 July 2025 18:40 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution Hi,
Yes that would be great what data do you need? All of the freesurfer output?
Best wishes
Samantha Hendry
Sent from Outlook for iOShttps://secure-web.cisco.com/1jITrGlBfvVxv_MV1yz4EADQssdmzO311rvsBFFb032yWp3yzWbcfo3fO5qanYltZKMDVTK1sQUa9eh6-0o22sSRiZqopDJhx80831fai0gIVKJ7JNz-V0V4aqlJv74eydSZzlZLIlwDCIwxukcp8t02Pu_t0uj9kNR0ewvFItut6BE4i7Qcr_LTTdeOoKniMABNLkmnmA8bdfnUwJ-iMTDv2648sN6Ggw_M9W2zUuKCW3hUUHeCbbQCjfzV4EMQYnN4wFDIfMsYOJVctbsmpGb59sa6QErnSOPmcoJHPqew-MXEsO4tHAvPejZGpknQHec3lbnK5gZEd0LLQUpK3Qg/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, July 29, 2025 4:48:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
You don't often get email from yhuang43@mgh.harvard.edumailto:yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1mb91cgj0OgjO89KXOyVtnqCW9kORHeHJIj4RZbwY2fpls0MoJkYrOcSMvkgqBoL_6CHyZ8M6BBNHOln5BTNA5J44j8Fov5h-0UPARIP1Ucnc0Y6ADNv2Ck7c8VugzQyQM-LmYfPAWyG8GZ8SgSaYY1LEzlCEEB4h0OapgOCChYUKm8k8KtXqZsSiSo6TCyZjhruwFHWmxIDwqdEw-BoBpbc69PnPaJELUAkvap4rrlEbUGKgKo5nEguMjPLZ3w9PvBm3JZqwn8meORclmYnGQEyMZ0vBoy2LhpS4MRs2L0smP7pIq42BewZacHvMhjcQ2GGRY_hkeXZJmBBa82cB9g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
If it is possible for you to share the data, we can take a closer look.
Yujing
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: Tuesday, July 29, 2025 10:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: Freesurfer stops are parcellation stats - segmentation core dumped
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From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edumailto:analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error.
#@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025
/exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz...
reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial...
reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 182364
Total vertex volume 180081 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Segmentation fault (core dumped)
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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2o6-IjfHYfI6zvjsGMfsxmclfev49n6DBAZc9WmJaGOkLcq4cjaXnmD0CCNQ-JCGR5gTKPpSNvw4yPr5dxn8lzb0JNSpdKJ905rBHuuFW-9uC7nXx31Ez0dC1ssWO5_GKNDppLrocZxj8X_m8ZYMKjtUBhxUlh04pg3eLSzE0fPaWVPTGsvORq9066H1VwxiiCLntQDvnp8q5dXRsHHDEGRH5MQSODT2L5iXHL-R69v9oJrWwOT5lN8FbjWYNrGlRm7vYnFnzLZt47i054BuYxcwfc1Bu02A6OIdvC6g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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.
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Hi,
Yes that is correct thank you for noticing it.
Do you know how I can do that run it on a Linux 7? Its okay I can look it up just thought I would ask you too
Best wishes
Samantha
From: Huang, Yujing YHUANG43@mgh.harvard.edu Sent: 30 July 2025 14:53 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
You don't often get email from yhuang43@mgh.harvard.edumailto:yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1DOq5XZKbexXIFQ-m3QWMOqndNgrxTpZxOxH5yhBrPxu4qC13sZJy54dDd-Tj_zMYKprpV2d9jyTaySlHqrS5qaHkZKGS8PM9RwhBnO5nuqifU_I5YIpg_azUml6DpcXkkNJNmLq3xwHqOTt8sHdA6QO_mYriAelnDLjbVzTr9iQdnCG22M0KQb3iI-FK52EBRZxQ92-iqhdB5YRftlKknRXTciHCTauM-EkfMteP5gBqpzBrnmMA51nT6PdpM14Bj_yK6pTo2_xA1uYsCfqrQASgr-QWjYAjkjeiGvcaiZBSEx1yI7cbbw5bIYqQz34PsgNQzxipuSjGZFlGTBbfeA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification You have sent two different recon-all.log. I noticed they were run on different machines.
The recon-all finished without errors was run on Linux7. The run failed with core dump was run on Linux9.
There are 3 runs in the recon-all.log with core dump errors: /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -i /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT1w.nii.gz -autorecon1 -noskullstrip /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -T2 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT2wreg2T1w.nii.gz -T2pial -autorecon2 -autorecon3 /exports/eddie/scratch/shendry2/freesurfer/bin/recon-all -s FMS_0094 -T2 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol/FMS_0094/FMS_0094_ABN_w0_20170316_3dT2wreg2T1w.nii.gz -T2pial -autorecon2-wm -autorecon3
'mris_anatomical_stats' core dumped for the 2nd and 3rd runs. 1st run finished without error but it didn't run mris_anatomical_stats'.
You are using FS6.0 built for centos6. It is possible the binaries are compatible with Linux7 but not Linux9. Before you send the files, can you try to run it on a Linux7 machine?
Yujing
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: Tuesday, July 29, 2025 5:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution Hi,
What would help to transfer specifically I am not sure how to send all of it?
Best wishes
Samantha
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: 29 July 2025 18:40 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
External Email - Use Caution Hi,
Yes that would be great what data do you need? All of the freesurfer output?
Best wishes
Samantha Hendry
Sent from Outlook for iOShttps://secure-web.cisco.com/1jITrGlBfvVxv_MV1yz4EADQssdmzO311rvsBFFb032yWp3yzWbcfo3fO5qanYltZKMDVTK1sQUa9eh6-0o22sSRiZqopDJhx80831fai0gIVKJ7JNz-V0V4aqlJv74eydSZzlZLIlwDCIwxukcp8t02Pu_t0uj9kNR0ewvFItut6BE4i7Qcr_LTTdeOoKniMABNLkmnmA8bdfnUwJ-iMTDv2648sN6Ggw_M9W2zUuKCW3hUUHeCbbQCjfzV4EMQYnN4wFDIfMsYOJVctbsmpGb59sa6QErnSOPmcoJHPqew-MXEsO4tHAvPejZGpknQHec3lbnK5gZEd0LLQUpK3Qg/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, July 29, 2025 4:48:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Freesurfer stops are parcellation stats - segmentation core dumped
You don't often get email from yhuang43@mgh.harvard.edumailto:yhuang43@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1mb91cgj0OgjO89KXOyVtnqCW9kORHeHJIj4RZbwY2fpls0MoJkYrOcSMvkgqBoL_6CHyZ8M6BBNHOln5BTNA5J44j8Fov5h-0UPARIP1Ucnc0Y6ADNv2Ck7c8VugzQyQM-LmYfPAWyG8GZ8SgSaYY1LEzlCEEB4h0OapgOCChYUKm8k8KtXqZsSiSo6TCyZjhruwFHWmxIDwqdEw-BoBpbc69PnPaJELUAkvap4rrlEbUGKgKo5nEguMjPLZ3w9PvBm3JZqwn8meORclmYnGQEyMZ0vBoy2LhpS4MRs2L0smP7pIq42BewZacHvMhjcQ2GGRY_hkeXZJmBBa82cB9g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
If it is possible for you to share the data, we can take a closer look.
Yujing
From: Samantha Hendry <shendry2@ed.ac.ukmailto:shendry2@ed.ac.uk> Sent: Tuesday, July 29, 2025 10:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: Freesurfer stops are parcellation stats - segmentation core dumped
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From: Samantha Hendry Sent: 29 July 2025 15:28 To: analysis-bugs@nmr.mgh.harvard.edumailto:analysis-bugs@nmr.mgh.harvard.edu Subject: Freesurfer stops are parcellation stats - segmentation core dumped
Good afternoon,
I am currently running Freesurfer for a group of subjects but I get the same error of segmentation core dumped when getting the parcellation stats stage.
This is a copy of the output and can attatch the recon-all.log of this error.
#@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025
/exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts
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
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz...
reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial...
reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 182364
Total vertex volume 180081 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Segmentation fault (core dumped)
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 -s FMS_0094 exited with ERRORS at Thu May 1 20:28:52 BST 2025
To report a problem, see http://secure-web.cisco.com/11-S0Vtbuvc_FsCRAQiUQv4d87PyEbUG2VlgwqvBqQv9HZDT...http://secure-web.cisco.com/131BJaXKVTNSvzwOvbztIF-rVEQtLQjwlAL2lKxiF0OHBMX2o6-IjfHYfI6zvjsGMfsxmclfev49n6DBAZc9WmJaGOkLcq4cjaXnmD0CCNQ-JCGR5gTKPpSNvw4yPr5dxn8lzb0JNSpdKJ905rBHuuFW-9uC7nXx31Ez0dC1ssWO5_GKNDppLrocZxj8X_m8ZYMKjtUBhxUlh04pg3eLSzE0fPaWVPTGsvORq9066H1VwxiiCLntQDvnp8q5dXRsHHDEGRH5MQSODT2L5iXHL-R69v9oJrWwOT5lN8FbjWYNrGlRm7vYnFnzLZt47i054BuYxcwfc1Bu02A6OIdvC6g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
As a note for the subjects i had to resample to the T1w scans to fit in with the 1x1x1 voxel size. Not sure if this ahs anything to do with it.
Any help would be so amazing really struggling with this.
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@nmr.mgh.harvard.edu
-
Huang, Yujing -
Samantha Hendry