Re: [Freesurfer] recon-all is shutting down? because of flair?

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_freev...

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

image.png

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

image.png





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