10/25/2017 at 7:20 PM #3634GavinParticipant
I am interested in making 3D figures (e.g., using Slicer) that incorporate the 3D drawings/rendered models of DBS electrodes that Lead DBS generates when one selects ‘render 3D’. Is there anyway to save or extract (as a nifti image, for instance) these electrode models for use in other programs? If not, is it possible to take the electrode trajectory/coordinates data and reconstruct the 3D electrode model using another software or plugin?
Gavin10/25/2017 at 8:19 PM #3635andreashornKeymaster
sure, just choose Tools -> Export -> .PLY which you can directly load into 3D Slicer or other apps.
Best, Andy10/25/2017 at 8:43 PM #3636GavinParticipant
Perfect, thanks very much!
Gavin03/17/2018 at 5:06 PM #4368canbeParticipant
I’m also very interested in making 3D figures. So I did “Export” and got .PLY files. And I opened these files on 3D slicer, but I couldn’t correctly overlay this figure on anatomical nifty file “anat_t1.nii”. The tips of electrodes, which actually exist in both thalamuses are overlayed on posterior lobes.
How can I match coordinate systems of these 2 figures, .PLY file and anatomical nifty image ?
And one other my question is how can I reflect the stimulated area by DBS on .PLY files.
I’m sorry to bother you, but I’m looking forward to hearing from you.
Sincerely yours,03/17/2018 at 5:27 PM #4369andreashornKeymaster
the .ply files are in MNI space.
You’d need to convert the coordinates to native space e.g. using ea_map_coords (but it involves some programming in Matlab).
Finally, visualizing VTAs – you’d need to convert the .nii files exported by Lead-DBS to surfaces – e.g. using isosurface() – and also export these as .PLY. These are in MNI space, though, too.
It’s all a bit involved and does require programming custom code + good knowledge about coordinate systems of nifti files and nonlinear warps.
If you prefer the 3D Slicer Render Engine over Matlab, one alternative idea could also to do the whole processing in Slicer instead of Lead-DBS? I know that the pyDBS software developed in Rennes / Paris is able to run inside 3D Slicer.
Hope this helps!
Best, Andy03/18/2018 at 12:33 AM #4371canbeParticipant
Thank you very much for your quick and kind advice !
I’ll soon try it.
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