it would be helpful to see some images. Also send the log file
On 11/9/2022 6:47 AM, dimitra kokkinou wrote:
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Dear freesurfer experts,
I am analysing some MP2RAGE images on freesurfer and found an error I
am unable to correct.
After the recon-all finished successfully, I looked at the T1 and
brainmask images on freeview and I noticed a skullstripping error on
the brainmask volume. On one side of the brain there was also skull
(and other non brain parts), and on the other half there was a lot of
missing cortex.
I tried to change the watershed threshold but this didn't work, I also
tried to put control points but most of them were ignored since they
were outside of the estimated pial surface.
What would be the best way to correct this problem?
Regards,
DK
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