thanks for your comprehensive answer.
So, comparing scrf and native coordinates, I can estimate the amount of brainshift, e.g. more than 4 mm in the antero-posterior direction in one patient:
-1.2301 4.3909 0.4404
Let me please ask one mow question. I’m curious why, if I apply the brainshift, I usually (in most patients) get electrodes missing the STN (fig. below, A), while when omitting the brainshift correction, the electrodes go thru STN, as expected (fig. B). The weird thing is that the brainshift correction seems to make sense for this patient (C), so it is not clear to me why it failed to make the position of the electrodes more accurate. Perhaps there is a problem with the normalization of the post-operative MRI (D)? Apparently, the post-operative MRI is not aligned with the MNI template well enough (D), while the pre-operative is (C).
Could you please comment on this? What would be the remedy for this situation? I would love to correct for the apparent brain shift, but the correction seems to make things worse.