Is there something I can do to extend the pial surface to include cortex that it ignored? In some places there are rather large chunks of cortex not included in the pial surface.
Link is to a screenshot, notice the top of the brain. It's fairly pronounced, visible in 12 adjacent sagittal slices.
I tried using the "Reposition Surface" tool, but I'm not exactly how it works, and I ended up just making the surface look crazy there.
I also tried adding control points in the white matter near the edges of the WM surface by the problem and ran the reconstruction, as someone in the archives suggested, but it didn't change the surface.
Thanks for your help, Eli
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