Hi Francois,
I noticed that the iEEG panel has been changed in the new BST version. However, the new panel did not show any electrodes. Moreover, the electrodes cannot be displayed as single circle contacts as before.
Can you please help on this? Thanks a lot.
Fang
Hi @fzp,
Thank you for reporting this.
To debug it better, can you share the steps that you are performing along with the MATLAB and Brainstorm versions you are using ? Also if you are using an old channel file can you share that as well ?
Thanks for replying.
I performed the SEEG/ECoG electrodes implantation in the BST and then saved the established channel file. But when i re-open the channel file (Display sensors->SEEG (cortex)), the iEEG panel showed no electrode information as above, though the electrodes were displayed correctly in the brain surface interface(as above) at the same time.
channel.mat (5.1 KB)
tess_cortex_pial_low.mat (1.4 MB)
Moreover, when I re-open my previous channel file, it showed the same problem. Now I cannot edit the iEEG electrodes and continue the related analysis in the GUI until the problem has been solved.
Thanks,
Fang
@fzp It is a bug at our end. We are working on updating it.
This issue has been fixed. Kindly update to the latest source code from GitHub - brainstorm-tools/brainstorm3: Brainstorm software: MEG, EEG, fNIRS, ECoG, sEEG and electrophysiology
Hi @chinmay.chinara,
I do have the same issue as @fzp , I have updated Brainstorm (just downloaded and started using version 23-Apr-2024) but electrodes are still not showing up in the panel for cortex view.
In addition I have spotted another issue related to plotting SEEG in anatomy since the last update (April 19 and now April 23 as well): when using the MRI viewer to display SEEG electrodes, it systematically overlays the CT on top of it. Same if I want to only look at the CT, the MRI is systematically overlaid on it.
Could you please help on this?
Thanks!
Angelique
Hi @avolfart,
I have updated Brainstorm (just downloaded and started using version 23-Apr-2024) but electrodes are still not showing up in the panel for cortex view
It works on my end with the data provided by @fzp above.
when using the MRI viewer to display SEEG electrodes, it systematically overlays the CT on top of it. Same if I want to only look at the CT, the MRI is systematically overlaid on it.
Currently we have the CT always as an overlay over the MRI. To just see the MRI, you can change the transparency of the CT overlay using the Surface > Data options > Transp slider.
If you just want to see the CT and MRI by themselves, in the anatomy mode, right click on the CT/MRI > Display > MRI Viewer
@avolfart if you have downloaded the binaries and source from Brainstorm download page then the updates we pushed today might not be reflected. Check this Version mismatch for compiled binary on BST website - #2 by Raymundo.Cassani.
You can download the latest updated source code from GitHub - brainstorm-tools/brainstorm3: Brainstorm software: MEG, EEG, fNIRS, ECoG, sEEG and electrophysiology and try running it again using MATLAB
Thanks for your reply @chinmay.chinara
I have clicked again on Update, re-downloaded the 23 April version, restarted the computer, it does not change anything...
For the cortex I get this (I show where I've clicked to get to that SEEG (Cortex) display for a given participant):
For the MRI and CT overlaid, transparency is already set at 0 (see screenshot) but I still get the CT artefacts from the SEEG shafts (only occurs on the two patients I processed since the update though). Here is how it looks like after clicking on SEEG (MRI viewer: EMU104_MRI_reslice):
Unfortunately I cannot provide you with the MRIs of my participants for you to check you on your side with my data. I can give you the channel location file if you think it can help though!
Note that everything worked correctly before the 19-April-2024 update.
try my suggestion above
the transparency should be set to 100 for CT to completely be transparent
I downloaded the latest BST version and found the electrodes information display correctly in the iEEG panel. However, i noticed that the SEEG (Cortex) display is always automatically accompanyed by the SEEG (MRI viewer) display. Close the SEEG (MRI viewer) display manually seems to arise error information in MATLAB. Can you try and fix this? Thanks a lot.
Fang
Yes opening up any surface in functional mode opens up the MRI viewer as well to aid towards better analysis.
What is the error that shows up ?
I apologize, I only saw your first post, not the second. I've downloaded the update directly from GitHub and it works now.
My bad... It works now 
Thanks again for your help and super fast replies!
Update your Brainstorm instance. This issue has been resolved.
Thanks a lot!
