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Hi Douglas, 

The cerebrum is removed and with no skull attached. 

However, compared to others that run normally,  it may have problems with white matter segmentation and missing brainstem (no clear). Attached the comparison below. Can you help figure it out?

Thank you so much!

Best, 

Qi 

On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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 

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Ph.D. candidate 

Icahn School of Medicine at Mount Sinai

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Ph.D. candidate 

Icahn School of Medicine at Mount Sinai

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