Hi Bruce,
Thanks for getting back to me. Unfortunately, we don't have a FLAIR/T2 for this subject. In some places the cortex is thicker than 8mm. I attached a couple screenshots. Is there somewhere specific that I can upload the file?
Best, Jonathan
[image: Inline image 4][image: Inline image 3]
On Fri, Nov 15, 2013 at 9:16 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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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