Hi John
does it come up in the correct orientation in freeview? If you didn't scan it in the orientation that a person would have been lying in the scanner, you will need to reorient the data so that we know what e.g. anterior is
cheers Bruce
On Tue, 26 Jan 2016, John Plass wrote:
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 tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm l), 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