Hi Freesurfers,

I have problems with the troubleshoot of a scan that didn't run at all within autorecon (while the scan actually looks good).

So I ran the skullstrip manually and came across the following phenomenon:

-when using waterthreshold 25 it gives me an error message and no brainmask.mgz file gets created

-when using waterthreshold 24 or lower big chunks of the brain go missing and most of the skull stays

I am not sure the manual editing will be a good approach as I would have to remove the complete skull

Any suggestions how I could get the skullstrip work?

Thank you,

Anne

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