Hello, I've been following the Ex-Vivo Recon instructions https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan of a formalin-fixated brain. With considerable manual editing, I've been able to produce convincing white and pial surfaces, but I am having trouble getting a good parcellation. The labels are reversed from anterior to posterior (e.g., superior parietal lobule area is labelled as middle frontal gyrus). I am assuming this has to do with problems with the surface registration. Also, when viewing the surfaces in Freeview, they appear pretty dark (perhaps similar to https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.html), although the correspondence between red/green and gyri and sulci appears to be correct. Might this be part of the problem?
Any advice would be much appreciated! If you'd like to take a look at the files, please let me know what and where to upload. Thanks very much for your help. Best regards, John Plass
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