you don't have to correct it. Slicer needs to be able to read it from the volumes and surfaces to properly display them. On Sat, 17 Jul 2010, Steffen Bollmann wrote:
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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