what do you mean you have a mesh in the original subject's anatomy in nii? Where did this come from? How was it created? If not from FreeSurfer, then there is no reason to think that they coordinates would line up. FreeSurfer uses its own (somewhat esoteric) coordinate system. I would be surprised if another package replicated it.

On 1/22/16 9:32 AM, Julia Berezutskaya wrote:

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

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