I'm new to Brainstorm and I'm working on an epilepsy protocol using invasive sEEG and cortical strip electrodes. I need to label the electrodes on the patient MRI (post-op CT with electrodes is already co-registered and overlapped). The tutorial I'm using to do this is the ECOG/SEEG tutorial (https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG) but it requires having the neural data already uploaded. I don't have neural data yet to upload but I still want to label the electrodes on the MRI. Does anyone know how I can do that?
There is a section dedicated to this in the sEEG/Epileptogenicity tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Editing_implantation_without_recordings
I recommend you also go through this tutorial, which illustrates different tools useful for handling sEEG and ECoG data.
Thank you for that link, i was able to manually place the electrodes. However, I know of this is a bug in the system or if I'm doing something wrong, but when I place the SEEG electrodes, the strip view only shows a line and not the individual electrodes. When I change to sphere view, the electrode marking disappears. As for the ECOG electrodes, neither of the views shows the electrodes on MRI viewer.
I would like to view the individual electrodes on MRI viewer to confirm accurate placement. Please let me know how I can troubleshoot this.
Also, how can I display the electrodes on the cortical surface viewer as well?
Thank you,
Isabela
You're supposed to see the contacts only in the MRI slices around them. Scroll through the volume to see them.
Or select the checkbox "MRI: Functional", it would display all the contacts across the entire volume projected on the current view.
The SSEG electrodes appear on every slide regardless of accurate anatomical location and even with the MIP:Functional checkbox unchecked:
When I select one of the cortical electrodes, the crosshairs show where I set the location of the first electrode, but there is not ECOG strip showing in that location:
How can I view the individual electrodes in both the SEEG and ECOG leads?
The SSEG electrodes appear on every slide regardless of accurate anatomical location and even with the MIP:Functional checkbox unchecked
This was a request from neurologist who didn't like the flickering of the SEEG electrodes when scrolling through the MRI slices. Therefore now the electrodes are visible all the way between their entry points to their tip.
When I select one of the cortical electrodes, the crosshairs show where I set the location of the first electrode, but there is not ECOG strip showing in that location.
When you select and ECoG item in the list of the tab iEEG, it centers the view of the MRI viewer on the point that you selected for this strip with the button "#1" at the bottom of the tab. However, the actual contacts might have been moved after setting this point, typically by projecting the contact on the skull surface. You should be able to find your contact a few slices away.
How can I view the individual electrodes in both the SEEG and ECOG leads?
Hide the ones the don't want to see: select them in the iEEG tab and click on the button "Show/hide selected electrodes":
https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Panel_iEEG
https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG#ECoG_strips:_IHA.2C_IHB.2C_IHC