Running in patient space only

[tsieger]

Hi,
would it be possible to use Lead-DBS to work solely in patient’s native space, please? For example, to reconstruct and extract stimulation electrode from non-normalized MRI, or compute VTA in native space? For now, it seems that reconstruction strictly requires normalized images.

My use case would be to reconstruct the electrodes in native space (before any non-linear mapping took place) and visualize VTA in native space too, superimposing the VTA on patient’s preop image.

Well, I understand that normalization would be needed to compute VTA (in order to know the distribution of WM/GM), or to show atlases, available in MNI, in native space (to determine the mapping between native and MNI space). But perhaps this would only pose “side steps”, while the main processing would take place in native space?

Thanks.
Best regards,
Tomas

[andreashorn]

Hi hi, yes, this already works – but you have to run the normalization once.
Then just visualize in native space instead of MNI and do your VTA calculations there.

[tsieger]

Thanks. Still, is it possible to extract electrodes in native space, in patient’s MRI being not affected in a nonlinear way?

[andreashorn]

Yes of course that’s a core feature of Lead-DBS. In the first popup under 7. Visualization simply choose native space and then 3D visualize which will be in native space. If you calculate a VTA there, it will be calculated in native space. You still have to run normalization to do so but the results will not be affected by this (only the atlas nuclei will be based on the normalization).

[tsieger]

OK, VTA can be computed in native space.
However, it seems that electrode reconstruction can be performed in normalized space only, as when I attempt to pre-reconstruct electrodes without normalizing first, it fails with: glpostop_tra.nii" does not exist., even though I choose the ‘Native Patient Space’ option under ‘7. Visualization’.
Maybe, I’m missing something.

[andreashorn]

Yes, you always need to run normalizations. However, that doesn’t mean they are actually used.
For prereconstruction, some of the algorithms need some waypoints that are defined in MNI space and then transformed to native space.
So again i) yes you will always need to run normalizations in Lead-DBS but ii) you can still use the native space reconstructions that do not really use the normalization and iii) if you use atlases in native space that are not manually reconstructed, the inverse of the normalization will be used.

Best, Andy

[tsieger]

Great, thanks a lot.
Tomas

[Author]

Posts