[Freesurfer] surf mm coordinates do not match the individual anatomy

Hi all,

I am loading a subject's surf (lh.pial) into MATLAB using read_surf(). At the same time I have a mesh based on the original subject's anatomy in .nii. The mm coordinates of these two do not match. Does anyone know why? The same anatomy was used for surface reconstruction.

The very ranges of vertex coordinates differ by 10-20 mm, and simple translation of coordinates along each dimension does not solve it. Most difference is along Z axis.

I understand, that along X axis it can be expected since there is only left hemisphere in surf and both in volume anatomy, but is there a way to coregister the other two dimensions?

Thank you,

Sincerely, Julia Berezutskaya