[andreashorn]

There was at some point someone however who had entered such a function inside the “Reconstruct Electrodes” function. Not sure if that still exists.

[andreashorn]

I don’t think so – you’d need to use code and apply the same transform to all entries, a bit like this (rename the ea_reconstruction.mat file to ea_reconstruction_unmod.mat):

load ea_reconstruction_unmod

shift=[7,5,5]; % shift to introduce to electrode (could be negative, as well).

for side=1:2
reco.mni.markers(side).head=reco.mni.markers(side).head+shift;
reco.mni.markers(side).tail=reco.mni.markers(side).tail+shift;
reco.mni.markers(side).x=reco.mni.markers(side).x+shift;
reco.mni.markers(side).y=reco.mni.markers(side).y+shift;

reco.mni.coords_mm{side}=reco.mni.coords_mm{side}+repmat(shift,4,1);
reco.mni.trajectory{side}=reco.mni.trajectory{side}+repmat(shift,size(reco.mni.trajectory{side},1),1);
end

save(‘ea_reconstruction.mat’,’reco’);

[andreashorn]

Hi Simon, I guess we never really continued work on Lead predict. It hasn’t really been released and shouldn’t be too helpful so far. We’ll work on some prediction tool at some point though.

Best, Andy

[andreashorn]

Hi, seems you don’t have the stats toolbox:
https://de.mathworks.com/help/stats/kdtreesearcher.html

Best, Andy

[andreashorn]

Hi Nabin,

see the install menu. It is merely for visualization and has been warped into 2009b NLIN ASYM space by us. So you don’t need to worry about registration. Once installed, it will be found in the backdrops dropdown of the 3D viewer.

Best, Andy

[andreashorn]

Hi Thomas,

since, v2.3, by default, VTAs are calculated in native space and warped to MNI. Thus, what you see as the deviation is the nonlinearity in the warp. Instead, the electrodes are modeled as a line always (at least currently). Thus, fit around the contacts is nice but not throughout the whole lead.

You should not see such a deviation in native space.

Re new topics, I guess the forum is a bit buggy and also much more buzz is in the Slack channel. Use that one instead, there are also way more people there to provide help.

Best, Andy

[andreashorn]

Hi Rubens,

this is a bug that we need to fix. These newer connectomes seem to work well with Lead mapper but not with Lead group. Thanks for letting us know!

Best, Andy

[andreashorn]

Hi Dan, good to hear from you, the message seems to be a warning only and should be fine.
If PaCER fails, maybe check whether patients that worked well on Mac fail or if it’s a problem of a novel patient. So far didn’t have OS-specific reports on Pacer functionality. If problem persists, maybe shoot Andreas Husch an Email or ask again in the Slack channel (see Help on our website) where Andreas is also active.

The community on Slack is much more active, maybe better to get help there in general :)

[andreashorn]

Great, thanks for the PR

[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

[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).

[andreashorn]

…one thing you could try re Shoot is to run DARTEL (which also builds the TPMs if they are not present). If that works, afterwards, Shoot should also work.
Have asked Ningfei & Simon to look into this, maybe one of them has some time for it.

Best, Andy

[andreashorn]

Hi Tomasz,

re contains: Would use a function called ea_contains and replace the calls to that. Should never name a function the same as built-in matlab functions. There aren’t many calls of contains in Lead-DBS.

Re Shoot, not sure, cannot debug right now. However wouldn’t really recommend shoot for DBS based on the Ewert 2019 Neuroimage article. Is there a particular reason you have to use it?

Can look into it somewhen but currently am on holidays.

Best, Andy

[andreashorn]

…based on the code, the keyboard should be deleted, so you can just run the next line to create TPMs.

[andreashorn]

Hi Thomas,

Great, thanks for catching this one. Would you like to submit a pull request that fixes the contains issue?
Re shoot haven’t used it in a while, would recommend to use ANTs.
But can have a look at it if I don’t forget.

Best, Andy

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