[andreashorn]

Hi hi, yes, this already works – but you have to run the normalization once.
Then just visualize in native space instead of MNI and do your VTA calculations there.

[andreashorn]

Hi Chris, unfortunately not (due to patient privacy restrictions).

[andreashorn]

Hi Josue,

there’s no official functionality for this. You’d need to manually edit the “markers” field in ea_reconstruction.mat. A few people have done this but it’s not really easy to explain and involves some Matlab skills :)
Hope you’ll be able to do it.

Best, Andy

[andreashorn]

…it will be created automatically once you visualize the atlas in 3D. Please also see the manual which covers importing new atlases.
Best, Andy

[andreashorn]

Hi hi,

I fear we’re also no experts with dicom imports, best ask the question in the dcm2nii forums.
I assume you have tried importing with all three methods already (dcm2niix, dicm2nii and SPM)?
Most likely the DICOM file is corrupted.

Best, Andy

[andreashorn]

Hi Kailaing,

I don’t know exactly what you did – depending on your settings. If you used a normative connectome, then it’s basically an atlas, of course, yes. If you used patient specific dMRI data processed in lead connectome, then you could think of it as classical fibertracking from the VTA (although we always first estimate the whole connectome and then select intersecting tracts from that).
Depending on your settings, the E-field is used instead of the VTA (and then tracts are weighted for Efield magnitude). Finally, depending on the analysis, lead dbs sometimes divides all counts by the total number of fibers in the connectome (resulting in small numbers) and even divides it by the size of the VTA (even smaller numbers).

It’s hard to tell what exactly you did from what you write.

Best, Andy

[andreashorn]

Gotcha, well, different thalamic nomenclatures still correspond to each other and an experienced neuroanatomist made these translations in the chakravarty paper (again see the same reference for more info on that). We adopted the dataset to complement the primary regions of interest (STN, GPi, GPe and RN) of the DISTAL atlas.

Best, Andy

[andreashorn]

Hi there, I don’t really understand what your question is.
The nifti files in the DISTAL (Ewert 2017) folder that have numbers (1.nii.gz etc.) follow the nomenclature of

Chakravarty, M. M., Bertrand, G., Hodge, C. P., Sadikot, A. F., & Collins, D. L. (2006). The creation of a brain atlas for image guided neurosurgery using serial histological data. NeuroImage, 30(2), 359–376. http://doi.org/10.1016/j.neuroimage.2005.09.041

But are also reproduced in the Ewert paper’s supplement.

Best, Andy

[andreashorn]

Hi Ben,

unfortunately not – this is a Matlab issue. I think we’ve googled and tried a lot of the “how to speed up 3D rendering in Matlab” web tips ourselves, already. If you’re visualizing a lot of tracts or stuff, maybe a different software like Trackvis can sometimes be better. Also can export electrodes with the Tools -> Export function to .ply format and visualize that e.g. using Blender, 3DSlicer or SurfIce (with any 3D viewer I think)..

Best, Andy

[andreashorn]

Hi Joey, sorry for the delay – any chance you can send me the lead group file so I could debug?

[andreashorn]

…if possible in the future open a thread for each question so it doesn’t get confusing.

[andreashorn]

Hi,

1. don’t understand. Maybe check the “Add Objects” menu and then “Add Roi”?
2. see https://netstim.gitbook.io/leaddbs/manual_correction_of_electrode_localization/how-are-reconstructions-stored
3. see the walkthrough tutorial on the website
4. no :)

Best, Andy

[andreashorn]

…it’s the DISTAL (Medium) atlasset.

Best, Andy

[andreashorn]

Hi Rubens,

I also just noticed that there was a serious bug in the ttest functionality in the “normalized” VTA reports.
https://github.com/netstim/leaddbs/commit/54fdc91f0570d442388f6030f58a56c9337ccf0f#diff-c406b0ce9f31d9fc6834ffef4b9e7f78R917
See this edit – if you need it now would need to change lines 917, 920 and 923 accordingly (or wait for the next update).

Thanks! Andy

[andreashorn]

No it should update like that.
You probably could update to 2.2 and test again?

Best, Andy

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