[andreashorn]

Hi, yes, you can check “map variable to VTA” and just set the variable to a set of ones. Then press visualize 3D.
At a later stage can add the result manually to a scene by choosing “add objects” > “add roi” in the 3D viewer. The sum of the VTA is stored in the lead group folder under /statvat_results.

Best, Andy

[andreashorn]

Hi RafDM,

sure, just make a new folder in the /templates/space directory and feed in the templates (e.g. t1.nii, t2.nii). Then you can copy/paste the file ea_space_def.mat file from the MNI_ICBM_2009b_NLIN_ASYM folder and adjust it accordingly.
Important is whether there is an FA template or not (hasfa=1 or 0), which anat_*.nii file will be mapped to which template (normmapping) and which is the default template (will be used for anat_*.nii files that are not explicitly assigned.

Best, Andy

[andreashorn]

Hi,

simply ignore the atlas_index files and just copy the according nifti files. atlas_index files will be automatically generated upon first visualization … and this will take a while.

Best, Andy

[andreashorn]

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

[andreashorn]

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and coregistrations, as well as brainshift correction highly during the last three years and new results (still unpublished) indicate that the choice of normalization method (or ANTs preset, etc) does matter drastically for DBS.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

[andreashorn]

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

[andreashorn]

Hi Vlevi,

we recently added a purely manual approach to localize electrodes in unusual targets that is currently only available in the github version (but will be released on the website at some point, too).
So if you’re in a rush, you can head to the lead-dbs manual and see “install via github” section – or wait for the next release.

Best, Andy

[andreashorn]

Hi,

I think this is documented in the manual and the Lead-DBS paper, also there’s a hint in the error message: Try setting entrypoint to manual first. Sometimes you need a few tries to get the lead in. Sometimes setting mask window from auto to a value between ~7 and 25.

Best, Andy

[andreashorn]

Hi Vincenzo,

I think this is an SPM issue – likely helpful to reinstall the newest version of SPM 12 and make sure that SPM runs smoothly.

Best Andy

[andreashorn]

Hi Gavin,

sure, just choose Tools -> Export -> .PLY which you can directly load into 3D Slicer or other apps.

Best, Andy

[andreashorn]

Hi mahsamalek,

nailing very atrophied brains to MNI can also be a bit dangerous – it’s a typical bias-variance problem (using a normalization approach that has high variance can lead to getting ventricles to fit but curly/smeary overfitting of smaller regions).
So in any case you should definitely check your data (e.g. take a look at the STN specifically in case of STN DBS) if you use a high variance normalization scheme.
I can recommend the ANTs preset “Effective (high variance)” as a first try.
Prelim data suggests that lower variance schemes do a better job at normalizing the STN though. So be careful with that.
And yes you need to upgrade for that normalization scheme.

Best, Andy

[andreashorn]

Yes, world-space (mm) is in MNI, voxels are not. This is a general neuroimaging thing that most people find confusing in the beginning (and some never bother to learn).. The image itself is aways a matrix with numbers and the header affine matrix defines where each pixel/voxel ends up in. Now a simple example is that you could build the same MNI space with small or large bricks. In the large brick version (say with a voxel resolution of 3x3x3 mm) voxel number 10 could end up at a coordinate of 30 mm, whereas in the 2x2x2 mm version it would end up at 20 mm. Now the header matrix makes sure the correct voxels end up in the same space.
To attain a very high resolution but small file size we export the vtas in a very high-res spacing but define the data just exactly around the VTA itself.

So yes you’re correct, it’s in MNI, but the data has a completely different resolution. Good neuroimaging viewers wouldn’t care and just overlay them. AFAIK fsl forces users to have everything in the exact same resolution (at least fslview does).

Best, Andy

[andreashorn]

Re the image orientations, please use SPM tools at least for initial reslicing to be on the safe side (lead-DBS treats stuff as SPM does).
You can e.g. generate full-stack high-res 0.5 mm MNI files (which will be huge) by applying:

copyfile(‘vat_right.nii’,’backup_vat_right.nii’);
ea_conformspaceto([ea_space,’t1.nii’],’vat_right.nii’,0);

the ,0 means nn interpolations, so maps will remain binary. Can do 1 for trilinear.

ea_conformspaceto(‘/path/to/your_mni_space.nii’,’vat_right.nii’,0);

will likewise reslice to the MNI space file you’re using.

Best, Andy

[andreashorn]

Hi Alexandre,

vat_efield_right.nii is the efield (values in V/mm)
vat_efield_gauss.nii is a Gaussianized or zscored version of that image (can ignore)
vat_right.nii is a thresholded map at the seceted value in the GUI (0.2 by default).

Best, Andy

[andreashorn]

Hi Alexandre,

vat_efield_right.nii is the efield (values in V/mm)
vat_efield_gauss.nii is a Gaussianized or zscored version of that image (can ignore)
vat_right.nii is a thresholded map at the seceted value in the GUI (0.2 by default).

Best, Andy

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