Import x,y,z coordinates

Hi Martijn,

I think this is doable and I recently tried, you’d need to write a script to generate the files ea_reconstruction.mat only. In these files, you’d only need to fill the variable:
reco.mni.markers.head and reco.mni.markers.tail
These should be the locations of lowermost (head) and uppermost (tail) contacts.

As far as I assume Lead-DBS will create the rest automatically once you localize the electrodes the first time.
To do so, you’d need to load up a blank folder which has only the ea_reconstruction.mat file and run the visualization step.

Hope this helps!

Best, Andy

Hi Martijn,

again, to do so, you’d need to load up a blank folder which has only the ea_reconstruction.mat file and run the visualization step.

It surely also makes sense to have some experience with the usual Lead-DBS workflow (e.g. localize one patient in Lead-DBS completely and get acquainted with the methods).
Moreover, we optimized normalizations and coregistrations, as well as brainshift correction highly during the last three years and new results (still unpublished) indicate that the choice of normalization method (or ANTs preset, etc) does matter drastically for DBS. So I can only recommend to use the Lead-DBS defaults over other methods (like FNIRT, DARTEL or a custom ANTs preset or similar, best in a multispectral way, i.e. feeding T1 and T2 in at least) for best results. But of course totally understand if you prefer to use your own preprocessing methods (in that case just put the ea_reconstruction file into a blank folder and select that one).

Best, Andy

Hi Martijn,

sorry, my bad! I didn’t realize how long we didn’t update the website version (since bigger new/revised features are in the making). I actually did only recently add compatibility with such manual localizations and it should work if you use the github version – or wait for the next release.
Sorry about that, didn’t think about it properly.

Best, Andy

Hello,

Looking to follow up on this old thread.

I am attempting to do a similar procedure as Martijn has described above but to be able to visualize the manually entered localization alongside an actual localization done with lead dbs through lead group.

I’ve followed Ningfei’s advice of setting up the reco variable for the manual entered localization and putting that into a blank subject folder, and that loads OK with the 3D visualization through lead dbs.

However, when I try to visualize the two localizations together in lead group, I get the following error:

_________________________________________________________________________________________
Cell contents reference from a non-cell array object.

Error in ea_showelectrode (line 34)
trajvector=mean(diff(trajectory{side}));

Error in ea_trajectory>update_trajectory (line 242)
[obj.elpatch,obj.ellabel,obj.eltype]=ea_showelectrode(obj.plotFigureH,obj.elstruct,obj.pt,poptions);

Error in ea_trajectory (line 159)
update_trajectory(obj);

Error in ea_elvis (line 164)
el_render(end+1)=ea_trajectory(pobj);

Error in lead_group>vizbutton_Callback (line 545)
resultfig=ea_elvis(options,M.elstruct(ptidx));

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_group (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_group(‘vizbutton_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

_______________________________________________________________________________________

It seems to do specifically with the manually entered localization as the lead group 3d visualization works fine if I just select the subject localized with lead dbs. I suspect it has to do with the fact that there is no further imaging/trajectory information available for the manually entered localization subject for the lead group script to use.

I am running matlab 2017b and lead suite 2.1.8.1

Thank you!
Joey

Hi Joey,

it seems like you can simply uncomment those lines (in general).
https://github.com/netstim/leaddbs/commit/51cdd3ba26ec1671d99b53657dcea6d2fa4f8d0c

Hope that fixes it!

Best, Andy