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
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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.