Hi Jonathan

it really depends on the characteristics of the dysplasia. We have some experience with this and in general FS does really well, but if it's a large region of cortex that is 8mm thick things will probably fail. Do you have a highres FLAIR/T2? That can help.

If you upload the subject I'll take a look
Bruce

On Sat, 9 Nov 2013, Jonathan DuBois wrote:

Hi All, 
I have run recon-all on a subject with a large cortical dysplasia, and while
the segmentation (aseg) seems to be relatively correct, there is a large
region of dysplasia not included by the pail surface. The normalized
intensity values for the cortex and the excluded region are very similar so
it seems that there is a threshold related to the distance from the white
matter surface to the pial surface, or perhaps normal gyrification that is
constraining the pial surface. 
Is there a recon-all or expert option for surface reconstruction of
abnormally thick cortex?

Thanks in advance, 
Jonathan

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