I don't know how that could have happened. Is the geometry of the
exvivo input oriented correctly? Ie, if you load the orig.mgz into
freeview or tkmedit, is sag actually sagital, etc?
On 01/26/2016 06:08 PM, John Plass wrote:
> Hi Bruce,
> Thanks for your reply. The orientation is correct in freeview,
> although, digging further, I see that that it is misoriented when I
> view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal
> --surf orig, and the orig volume is shown oriented correctly, but the
> orig surface appears to have some of the dimensions swapped. Any idea
> why this might be?
>
> Thanks for your help!
>
> John
>
> On Tuesday, January 26, 2016, Bruce Fischl <fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> 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
>
> <http://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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> --
>
> ---
> John Plass
> Ph.D. Candidate
> Visual Perception, Neuroscience, and Cognition Lab
> Northwestern University
>
>
>
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