Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview the same (or similar?) problem occurred: (volume: orig.mgz (http://dl.dropbox.com/u/1263357/orig.mgz) ; surface: rh.pial (http://dl.dropbox.com/u/1263357/rh.pial)) screenshot: http://dl.dropbox.com/u/1263357/cras_problem_freeview.png
It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
you are right: the c_ras is non zero in orig.mgz: -2.57772 14.6127 -8.48792
Is there a way to correct that cras -value? (I need to to further processing in a small and unknown software, which is based on VTK and this shows the same issue - might this even be a problem in the VTK-framework?)
Thank you Steffen
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
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