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Hi,
I am trying to manually correct some segmentation errors through Freesurfer. In particular, I have noticed a number of areas where the pial surface appears to miscalculated and is excluding chunks of grey matter. I tried using control points to push the
pial surface out, and this helped reduce the grey matter exclusion, but now there are many places where the white matter surface has been reconstructed too far out, such that it includes a bunch of true grey matter within the white matter territory. Is there a way that I can combine the original white matter surfaces with the corrected pial surfaces? When I tried to combine them in this manner and run recon-all, I received an error suggesting that the surfaces needed to match. Did I interpret that right,
and is there a way around this?
Also, do you have any recommendations as to how I can extend the pial surface to correct grey matter omissions without incurring new errors as a result of the correction method?
Thank you for your time and help.
Kalyan
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