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.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

 

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Hi,

 

Yes that would be great what data do you need? All of the freesurfer output? 

 

Best wishes 

 

Samantha Hendry 

 

Sent from Outlook for iOS

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

 

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.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/BugReporting

 

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

 

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