Hello FreeSurfer Developers,

I'm attempting to run freesurfer on a resampled T1w scan and it has come up woth segmentation fault error at the stages of the atlas. This is the full error when I just run recon-all from the start:

#@# 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)

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 node1c26.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