You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

On 6/24/2024 12:42 PM, egemen gok wrote:

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Thank you for your response. Okay, one more update. I tried recon-all for patients with T1.

Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.

I need to process this dataset for a huge study of our faculty. I hope we can fix this.

Kind regards

Egemen

Douglas N. Greve <dgreve@mgh.harvard.edu>, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:

Can you attach the log file. I can't read the pics you attached

On 6/18/2024 10:56 AM, egemen gok wrote:

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Hello Freesurfer Developers

recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)

and fyi = I used flair image because there was no T1 image of the patient

and this is the log file (recon-all.log) =

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