[andreashorn]

Dear Kristen,

sorry for this bug since it has already been reported (need to fix it soon). A workaround is to download the group connectome found here (http://www.lead-dbs.org/?page_id=317) and install the files after unzipping them into the lead/fibers folder.
It’s just that at present lead_group needs these files for the UI elements to work properly.

Please let us know if other errors occur since lead_group is still a a bit buggy and not well tested by many users yet.

Best, Andy

[andreashorn]

Dear melanogaster,

This could actually result from a quite old version of Matlab (2009b) not recognizing figures made with a newer version (2015b). I am not sure about backward compatibilities.
To the best of my knowledge, lead dbs should run with anything ~2011 on and doesn’t need many toolboxes. statistics, image processing if any.
We try to develop lead using least possible toolboxes.

Best, Andy

[andreashorn]

Dear Robert, you are completely right. The Pallidum is already covered by the GPi and GPe parts. I’ll fix this in the next update. You can rename the files yourself but need to also delete the atlas_index.mat file in the BGHAT folder to let lead re-extract the info from the nifti files.
Thanks for the hint!

[andreashorn]

Okay – I have made the same experience with MPRAGEs before, also T1 doesn’t seem to be as well suited to reconstruct the trajectory, but in general it seems to work for me. In some cases, you can’t delineate all 4 contacts of both electrodes, however, sometimes the uppermost contact seems to show a slightly larger artifact. Since the contacts are equidistant, this might help to place the contacts correctly. Also, you might want to estimate the distance between the electrode contacts, which is usually slightly greater than 2 mm (or 3 mm in 3387 electrodes) depending how much warping has been done in the normalization process. The distance should be displayed in the Manual Review window.
When doing the first reconstructions, I agree that it sometimes feels a bit difficult where to exactly place the contacts, but after about 10 reconstructions, in my experience one gets a confident feeling about where to put them.
If you happen to have some imaging data from 3387 electrodes, it might be easier to start with those as well.
But in any case I’m happy that there were no further technical errors so far.
Best, Andy

[andreashorn]

Hi Marcus,

thanks a lot for reporting this typo! I have fixed both errors and am uploading an update at the moment.
In theory, there should be an “Update” button in the top row of the lead-GUI and you can press it to download the update.
If not, you can run ea_update(‘force’) to do so.

Did the rest of the process work for you so far?

Yours, Andy

[andreashorn]

Dear Marcus,

I’m sorry for this error, most of all because I’ve known about it for some time now and should definitely fix it soon. The problem is that lead tries to use some builtin Matlab functions but instead uses functions supplied with fieldtrip (part of SPM) which have the same name.
The functions in doubt should be located here:
spmfolder/external/fieldtrip/connectivity/

and are called nansum, nanmean and nanvar.

A quick-fix would be to just rename these functions (maybe append a _ft to them or something temporarily) and the whole thing should work again. If you are a fieldtrip user, it might get a bit complicated since I guess that fieldtrip will need these versions for some connectivity analyses.
I will fix this issue in an update soon.

Yours, Andy

[andreashorn]

Dear Petra,

I will sooner or later write a function that is able to plot group results in 2D, but as you, I am not sure, how best to do so. What you could do in the meantime is load the contacts as fiducial points in slicer and load up an MNI template to visualize the whole thing.
You can also use the Lead 3D-viewer and in the axis panel select e.g. X-Cut instead of 3D view. It will then simply crop the 3D-figure to a cut. You can select to display electrodes as point clouds only in lead_group and could even tell the program to only show the ventral contacts by making them the only “active” contacts.
lead_group is still quite complicated, so we could maybe best skype briefly to do so together, if you’d like to try that.

Yours, Andy

[andreashorn]

Hi everybody,

in the future, please open up a new discussion for each question, otherwise, this might get a little difficult to read later on!

Thanks!
Andy

[andreashorn]

Hi Jose,

The normalization routines of DBS use (sometimes slightly modified) SPM methods and you could also choose to start off with normalized images directly (normalize them to MNI space using SPM, FSL, Slicer, whatever works). You just have to rename the normalized files to “ltra.nii” and “lpre_tra” respectively.

You can use the accumbems from the HO atlas, simply isolate it from the atlas file for right and left hemisphere (e.g. Using image calculator) and put the files in a new atlases/subdirectory in /lh and /rh subfolders (or /mixed if you only have one file for lh and rh together). It should then pop up in the toolbox automatically.

Hope this helps!

Andy

[andreashorn]

Dear Petra,

this is a tough question since there is no real ground truth if you can’t see the contacts. You can try to adjust the contrast and brightness levels in the review window and try to see if you can determine the contacts. My experience is that one can see the single contacts better in mr images.

Another alternative is to double check in a different viewer after you have saved your reconstructions.
If you use Slicer in the version 3 (I have version 3 and 4 installed simultaneously on my computer), you can directly read in the .fcsv file Lead generates as fiducial points. You can overlay these points onto the image and adjust the contrast of the image better and more accurately in slicer than in lead. If you are lucky, you can see the single contacts there.

If you dont want to use slicer 3, you can also manually place some fiducial points in e.g. slicer 4 and enter the coordinates from the .fcsv or the ea_reconstruction.mat file manually.

I guess in general your heuristic is not quite wrong given the architecture of the electrodes and my own experience. I have analysed some patients that had both CT and MR postoperatively taken and could directly compare the results between MR and CT. Going ~4 steps up is at least a rough heuristic and the distances we talk about are probably quite small (i.e. within image resolution magnitude).

However, if you can’t really see all 4 contacts, you can also only guess how the spacing between the contacts changed due to the normalization procedure. If a patient’s anatomy is e.g. stretched a lot in z-direction to fit the template’s anatomy, the between-contact spacing of this patient within MNI-space should also be larger than the actual electrode spacing (e.g. 2 mm for most makes).

I hope this helps!

[andreashorn]

Dear Johannes,

thanks for this feedback and for trying out the toolbox! We already realized this on a windows machine and adapted the GUI, which has been made on a mac, a bit. However I took the opportunity to re-model the whole GUI to have more space and to get a clearer overview of the workspace this morning. I also entered some tooltip-strings, so if you hover over the GUI elements now, there should be some help displayed. I’ll send you a download-link for the new version soon. Please tell us if the GUI still feels crumpy, because this is very important for the overall user experience, of course.

Cheers, Andy

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