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Hi Shai,
this usually happens when niftis are not in standard nifti orientation and maybe were not imported from DICOM properly. Please make sure to do the DICOM import with a new version of Lead-DBS.
Also maybe try to make some experiences with other datasets that work first.
Finally, if it all persists, trick is to manually prealign volumes to MNI space (e.g. using 3D slicer) first and then run Lead-DBS based normalization – but this is pretty involved and cannot be explained easily here.Best, Andy
Hi Michael,
please ignore the surface recon step for now – it is not functional. We should have hidden it in the public release, are working on that currently.
Best, Andy
Hi Arianna,
weird – seems like your files have the wrong filename?
Please check if you do everything as in this walkthrough video.
Hi Arianna,
the normalization didn’t run through, probably because your computer doesn’t have enough RAM. Please try to normalize with SPM Segment instead (which is equally good and much faster).
Also you need to choose between either postop MRI or CT (using both is not possible), so choose the one with the better resolution (which is usually the CT).
Best, Andy
No, depending on the model, they are not spherical and the local tissue properties are used to inform them.
For your purpose maybe the Mädler & Coenen model is helpful which gives you a diameter depending on Voltage and Impedance.Mädler, B., & Coenen, V. A. (2012). Explaining Clinical Effects of Deep Brain Stimulation through Simplified Target-Specific Modeling of the Volume of Activated Tissue. AJNR American Journal of Neuroradiology. http://doi.org/10.3174/ajnr.A2906
Function that calculates the R is maedler12_eq3 inside ea_genvat_maedler
-> In case you want to get more familiar, why not have a look at this walkthrough video: http://www.lead-dbs.org/helpsupport/knowledge-base/walkthrough-videos
It’s not too complicated :)Hi there, you can create niftis with spheres at these sites maybe using FSL or other neuroimaging tools.
Then you can import them into the Lead-DBS viewer using the “Add Object” menu.
But in general, it’s not too easy to import things if you’re not really familiar of how Lead-DBS stores stuff etc.
Usually much easier to relocalize the electrodes quickly if you’re familiar with it.Best, Andy
Hi Arianna,
it seems like you didn’t install Lead-DBS properly. I would suggest to redownload from the website, unzip and then only add the base folder (without subfolders) to the Matlab path. Then run “lead dbs”.
This should work..Best, Andy
Hi Zhaoyu,
sure – please have a look at the walkthrough video:
Then it also makes sense to read the related paper to know what the promises and limitations of our VTA model are (Horn & Li et al. 2018, NeuroImage): https://www.ncbi.nlm.nih.gov/pubmed/30179717
Finally, the VTA nifti files are stored under the /stimulations subfolder in the patient directory after you created them. They are usually in MNI space.
Best, Andy
Hi Nabin, weird!
So you see the stimulation in mapper and you selected it, right? It also has bilateral VTAs (could be that it only works with bilateral ones)? And mapper finds the connectomes right?Hi Nabin,
it could well be that the functionality in this (point 1) is currently broken – we’ll investigate and hopefully push fixes to github soon.
Re 2. – not really but you can easily create your own atlases (i.e. combine two) by just creating a new folder with the according nifti files inside (don’t mind the ea_atlas_index.mat and the gm_mask nifti file, these will be generated upon first visualization of the atlas).
3. 2D view is neurological convention (meaning left is left and right is right). Instead, some other programs follow radiological convention (where right is left and left is right, “view from below”). 3D view is not flipped (in 3D it’s all more clear and obvious).Best, Andy
Hi Adino,
it’s surely not the version number, this should be fine.
Regarding screenshots, the best way is to use our Slack user channel:There are also more experts online there than here, maybe someone else has an idea.
Thanks!
Best, Andy
Hi Aidno,
I fear I can’t say much to help you based on the things I know.. We have over 7000 downloads and it usually just works. I’d make sure there is only one single lead-dbs folder on your hard-drive (delete everything older or so). Make sure you have SPM12 on your Matlab path. Also make sure you have ML version >= 2015b.
If that doesn’t help, do you have a Matlab expert somewhere in your institute who could have a look at it?Best, Andy
Not sure why and this has not been reported before. Again, I’m pretty sure that you don’t have all files and should make sure you have a full install. Maybe you just lack some data files. I would redownload, delete the old folder and try again.
Best, Andy
Hi Aidno,
just make sure you have a proper installation of Lead-DBS, then it should show the DISTAL atlas by default.
See https://leaddbs.gitbooks.io/leaddbs-manual/content/Installation.html for a guide on how to install Lead-DBS.Best, Andy
