Hello,
We have a large number of subjects processed with the default settings of recon-all. Unfortunately the presence of white matter creates problems when creating the white matter surface. There are large hypo-intensities in the white matter which badly distort the surfaces in multiple areas of the brain. It is unfortunate because these areas seem to have about the same signal intensity as true cortex, leading to a confused algorithm, and very pronounced segmentation errors.
I have been manually editing and reconstructing these surfaces, but the process is tedious and error prone. Are there any flags that might help recon-all perform better on brains with white matter pathology? Or otherwise things that I can do to make fixing the segmentation less painful?
Thanks, Eli
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