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> 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 > > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- --- John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University
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