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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UNIVERSITY OF CAPE TOWN
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