[tsieger]

Dear Andy,
sure, I’m sending a link to the patient folder data directly via email.

Yes, I’m using the latest version of LeadDBS 1.6.3.4, with the hotfix from 2017-06-12 morning applied.

Best, Tomas

[tsieger]

Oops, I accidentally swapped some pictures in the figure above, and made the text of my previous post #2721 confusing. I’m very sorry for that.

The figure above is OK now, and the corrected problem description is:

If I apply the brainshift correction, I usually (in most patients) get electrodes missing the STN (fig. B), while when omitting the brainshift correction, the electrodes go through STN, as expected (A). The weird thing is that the brainshift correction seems to make sense for this patient (C, green arrows), so it is not clear why the correction moved the electrodes away from the STN. Perhaps there is a problem with the MRI normalization? Apparently, the post-operative MRI is not aligned with the MNI template well enough (E), while the pre-operative is (D).
What would be the recommended way of dealing with this problem? Shall I perform another MRI normalization? Shall I omit the brainshift correction? (Of course, I would like to have the position of my electrodes reconstructed as accurate as possible, so I would like to perform the correction.)

Thanks, Tomas

[tsieger]

Hi Andy,
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:

>> a.reco.scrf.coords_mm{1}(1,:)-a.reco.native.coords_mm{1}(1,:)
ans =
-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.

Thanks.

Best, Tomas

[tsieger]

Hi Ningfei,
thanks for your quick reply. Yes, the steps you suggested resolved the issue.

(And the hotfix I applied later on also solved this warning, which appeared after setting the color manually:

“Warning: The LineSmoothing property will be removed in a future release.
> In ea_writeplanes (line 316)

)

Thanks a lot!

best,
Tomas

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