External Email - Use Caution
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 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.