I don't think resampling should have caused this error. Can you look at the aparc? Eg,
cd $SUBJECTS_DIR/FMS_0094
tksurferfv FMS_0094 lh inflated -aparc -label labe/lh.cortex.label
The cortex label will appear as bright yellow. Make sure it look ok, meaning everything covered except the non-cortical portions of the medial wall
Then remove the label so that you can see the aparc. It should cover all the same parts as the label.
You can also just look at the surfaces to make sure they are ok, eg,
tkmeditfv FMS_0094 nu.mgz -surfs
Does it happen for all your subjects or just this one?

On 7/25/2025 2:40 PM, Samantha Hendry wrote:

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Hello FreeSurfer Developers,

 

I'm attempting to run freesurfer on a resampled T1w scan and it has come up with segmentation fault error at the stages of the atlas.

 

I was wondering if the resampled T1w scan has caused this error and this is the only difference between processing before. I am really stuck and its not a system compatability issue as I have been able to run all of my freesurfer output without error before so anything would be great.

 

 

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 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

4) recon-all.log: see attached

 

Not sure if the above is fully correct. Any help would be greatly appreciated!

 

Best wishes

 

Samantha Hendry

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