I see. Sorry I don't know the details of the vtk surface file format. Maybe Ruopeng does? Does it store ras2vox info? On Mon, 3 Sep 2018, M. Jordan wrote:

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Yes, when I import the original file (lh.pial) and the converted .vtk file (lh.pial.vtk) in Freeview, there is a mismatch. I am using the vtk pial file in a C++ application to visualize the brain. Now I want to import the CT NIFTI into  this application to extract the iso-surface using a marching cubes algorithm. In order to avoid transformation  matrices etc. it would be great to process the CT NIFTI in such a way that it matchs the converted vtk files.

Thanks for your help.

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Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Bruce Fischl fischl@nmr.mgh.harvard.edu Gesendet: Montag, 3. September 2018 22:16 An: Freesurfer support list Betreff: Re: [Freesurfer] NIFTI to pial.vtk space   How do you know it is shifted? Do you visualize it in freeview? And what are you intending to do with the CT? Maybe you are better off sampling it onto the surface than trying to map the surface onto the CT? On Mon, 3 Sep 2018, M. Jordan wrote:

...

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Hello,

I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. When I export the .pial files

to

...

.vtk using mris_convert, they are shifted with respect to the MRI. Is there a way to process the

CT

...

NIFTI in such a way that it will match the .vtk pial files?

Thank you!