Getting contact positions in MNI space

[cloz]

Hi there,
I was just wondering if there is any way to get the position of the contacts/electrodes after they have been constructed in lead DBS. Also is there any way I could get the electrode as a nifity file?

Thanks,
Chris

[andreashorn]

Hi Chris,

the ea_reconstruction.mat file stores the data (or in lead group the LEAD_groupanalysis.mat file). In the former, the variable reco stores the data.

For instance,

reco.native.coords_mm{2}(3,:)

will be the left ({2}) third lowest (3,:) contact coordinates (x, y, z) in native (i.e. postop_tra.nii or rpostop_ct.nii) space.
Similarly, reco.acpc is an automatic (Horn et al. 2017 NeuroImage) transform to AC/PC space, whereas reco.mni is in MNI space. Finally, if you did run brainshift correction, there will be a fourth entry called reco.scrf which will be in anat_*.nii space.

Regarding a nifti of the electrode, a lot of people are asking for this and we’ll program it in at some point but for now there’s no readily available function doing this. You can export electrodes as vector files (in the Tools menu) and potentially convert to nifti (maybe with 3D Slicer but not sure, never tried). If you know some ML coding, it shouldn’t be too hard to write out a nifti file yourself.

Best, Andy

[Author]

Posts