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
>
>
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