[Freesurfer] Freesurfer flips brains?

Dear all,

I must be missing something really obvious, but it seems my brains are flipped. What I do:

- I have a highres structural scan, nii file format - I convert it to a surface using recon-all - Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans - I try to bbregister the coregistered and resliced T1 with the surface

But then: hey, it doesn't fit, my low-res T1 is flipped compared to my y surface, hence to my original T1. So is it indeed true that my T1 might have been flipped? If so, does it make a wrong assumption on neurological vs radiological convention, or what is going on?

Thanks in advance,

best,

Frank