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Dear Freesurfer Developers,
I must admit that I have not used Freesurfer for quite some time, i.e. I may be a little rusty. I vaguely remember having the same issue a few years ago, but I cannot find anything in the forum that seems to work for me. Hence, I apologize for a potentially trivial question:
I am having problems with mris_convert when trying to convert a surface from FS format to .vtk. It seems that during the conversion the orientation of the surface is somehow changed to what looks like a rotation by 90 degrees (indeed the file information seems to suggest a [x,y,z] <-> [x,z,-y] transformation).
For instance, after running "recon-all" on a standard MNI152 brain (here borrowed from FSL), I want to convert the pial surfaces to .vtk format for further processing. I use the following simple command:
mris_convert lh.pial.T1 lh.pial.T1.vtk
Opening both surfaces in, for instance, freeview shows lh.pial.T1.vtk somewhat rotated by 90 degrees. Other target surface formats have the same issue. My suspicion is that there is some intrinsic orientation change during the conversion. How can I preserve the orientation during mris_convert? Wouldn't that be the expected behavior? Alternatively, how can I change the orientation of a surface file after the conversion?
Thank you for your advice!
Best, Aicko
---- Dr. rer. nat. Aicko Yves Schumann Research Assistant Professor Physicist, Center Statistician, Big Data Scientist Institute of Psychiatry Medical University of South Carolina 67 President Street (Rm. BA506C) Charleston, South Carolina, 29425 United States Phone Office: +1 843-792-6470 Phone Cell: +1 843-532-8506