Hi Jonathan
I think it's more likely the noise within the cortex that is messing
things up - the very bright voxels that are just outside where the surface
settles. Freeview has a "reposition surface" tool you can try - maybe with
a larger sigma. Can't remember what the default is, maybe 2. Try some large
ones and undo the change if it looks bad
cheers
Bruce
On Fri, 17 Apr
2015, Jonathan DuBois wrote:
Hi Freesurfers,
I am having trouble manually correcting the surface of brain with an
abnorally thick cortex due to a malformation. It seems as though there is a
thickness threshold that constrains the pial surface reconstruction. I have
added control points to the white matter but the problem seems to be due to
the adnormally thick cortex or the abnormal gyrification. Is there an option
I can change when running recon-all or a manual edit I can make in these
cases? I understand that it may not be perfect but I would like to get it
good as possible.
Thanks in advance,
Jonathan
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