Hello Freesurfer Experts, I wrote in recently about my parcellation troubles with an ex-vivo scan ( link <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45181.html>). Digging further, I've found that the surfaces I've produced following the Ex-Vivo recon instructions <https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon> are oriented properly when viewed in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID orig.mgz rh.white). I suspect that something related this might be the source of the parcellation problems. Any idea why this might be and how I can fix it?
Relevant background information: *volumes were reoriented before FS processing using the command "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz" *running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04 As always, I'm very grateful for any help you can provide. John
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