You should look at the wm.mgz to see where the defect is. Probably cerebellum is still attached or maybe a big piece of skull.

On 5/4/2020 11:19 PM, Zeng, Qi wrote:

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Hi,

I've conducted longitudinal T1 recon-all. One subject's last-scan ran into error in the first independent recon all step: " recon-all -s SUBJ1 -SUBJ1.nii -all'.

Error: "CORRECTING DEFECT 0 (vertices=14101, convex hull=2297, v0=1419) XL defect detected...". Log file attached below.

I've increased the memory usage limit as some suggestions did, but no help. Also T1.nii looks fine, same parameter setting as first scan, also attached below. Subject first scan and all the other subjects were finished without errors. Can you help figure out what has caused it?

Thank you so much!

Best,

Qi

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai
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