[andreashorn]

Hi canbe,

thanks for your nice words. I fear I don’t understand what you want to do. Diffusion tensor images (you made with FSL) should be suitable for FSL. Then usually .nii images are 3D (or 4D) but usually not 2D.
Lead-DBS is mainly for reconstructing DBS electrodes. You can in theory use Lead Connectome to perform whole-brain fiber tracking and then investigate connectivity from DBS electrodes to other regions. However, this process is poorly documented and most people that know how to do this currently lack the time to write nice tutorials about it.

Best, Andy

[andreashorn]

Hi Markus,

I guess you’d then need to set writing permissions to the folder in which your Lead-DBS version is installed. Do you know how to do that? Matlab needs to be able to save variables into that folder.

Best, Andy

[andreashorn]

Hi, should be there but please update to the newest version first. Also only appears if you show electrodes (i.e. a patient is selected with reconstructions made).

[andreashorn]

Hi Alexandre,

we were planning to release our new VTA model (that allows bipolar settings) much sooner but it hasn’t been released so far. It should be a matter of weeks now. The currently available models (Mädler / Kuncel) only allow monopolar simulations (also see their papers).

Sources are usually not needed but could be any independently modeled sources of voltage (e.g. the Medtronic “Interleaved” setting could be modeled with these or the Boston Scientific settings that could later be modeled with our new model).

So in brief: Currently only monopolar stim is possible but bear with us for just another 2-3 weeks for Lead-DBS 2.0 to come out.

Best, Andy

[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

[andreashorn]

Hi,

that’s a simple reslice.
E.g. use

ea_conformspaceto(‘anat_t1.nii’,’vta.nii’);

Of course you loose resolution with this and the above command replaces vta.nii – so make a copy first.

Could also use SPM, FSL or any other neuroimaging software to do this.

Best, Andy

[andreashorn]

Hi Jen,

sorry for the late response. You can create a VTA in native subject space (just open the 3D visualization tool in native space and create a VTA). The VTAs are saved as nifti files in patientfolder/stimulations/stimulationname/vat_right.nii and /vat_left.nii

These files are in space of your anat_*.nii, postop_tra/cor/sag.nii and rpostop_ct.nii files.

From there, it’s standard neuroimaging stuff, if new to this let me know and I can explain a bit better.

If you’re familiar with any standard neuroimaging pipeline (e.g. SPM or FSL) you could use it to coregister your anat_t1.nii to your b0.nii and port the VTA to DTI space that way. Then extract the values of FA under the mask.

Makes sense?

Best, Andy

[andreashorn]

Hi elliot,

currently, there’s no function for that. You can export the trajectories to surface formats via the [Tools] [Export] options. Then probably there’s some way out there to convert to nifti (maybe 3D slicer can do it?).
A few users have asked for this already, so we might end up doing it at some point. But I fear it’s not high priority currently.

Best, Andy

[andreashorn]

Hi cloz,

unfortunately, unilateral leads are not really reported, especially not in Lead group. Sorry about that, we just never had a real project with them so there was no need to support them up until now.
I fear you need to write custom code for the group level stuff.
On single subjects, in the rare unilateral patients I visualized so far, I usually just place two leads in and ignore one of them (deselect in 3D viewer). But I fear – depending on what you aim to do in lead group, it won’t really work.

Best, Andy

[andreashorn]

Hi cloz,

you can change the height in the ea_spacedef.mat file in /templates/space/MNI_ICBM_2009b_NLIN_ASYM
or in the code at ea_reconstruct_trajectory > ea_getstartslice on line 312.

A postop T2 is definitely easier to reconstruct the lead if the lead crosses the ventricles (since in T1 both are dark).

Hope this helps!

Best, Andy

[andreashorn]

Hi cloz,

the red area doesnt need to overlap with the artifact, it just shows you the side you need to click on.

Should work ez&well with Fornix electrodes.

Best, Andy

[andreashorn]

Hi Chadwick,

I’m not sure if it would make a difference since we use linear registrations in these steps. My feeling it that rather the risk of failed coregistrations increases if one has multiple cascaded registrations. But I don’t have any data to support this claim.
I think the “brainshift correction” tool in Lead-DBS should remove any pre- to post inaccuracies, especially if using good quality data.

Regarding postop MR vs. postop CT, this is an ongoing debate and I have not decided. I used to prefer MRIs over CTs since one can verify position in native (postop space), sometimes directly identifying the STN or other structures. I guess the advantage of CT is higher resolution re placement of each contact of the electrodes. Although one can visualize them with multiple MRIs, pretty good as well.

Hope this helps?

[andreashorn]

Hi canbe,

sure, this should be possible. Can you visualize it in MNI space?
If this works and the normalization is accurate, you should also be able to visualize in native space.
After that, you could also put in manual segmentations into the atlases/ directory in the patient folder – but let’s go step by step first.

Best, Andy

[andreashorn]

Hi Vinny,

the PaCER method is not published and what you’re seeing is just an interface to it that we are developing. You seem to be using Lead-DBS in “Dev-Mode”. Please open your preferences files and set prefs.env.dev=0.
It can sometimes be risky to use dev mode for a productive system since also other parts of the code could then be rooted to code that is unstable or sometimes even wrong. So I really would not advise you to do so :)

Best, Andy

[andreashorn]

Hi Vinny,

sorry for that!
It’s easy to fix, you only need to click on the Settings button next to the ANTs normalization name (the popup menu where you choose the normalization routine) once and choose a setting. Then it should work.
The default name changed and we forgot to update that. Thanks for letting us know!

Best, Andy

[Author]

Posts