sEEG: electrodes localization. How to visualize sEEG electrodes on MRI?

[anaisservais]

Hello,

I am conducting a study on sEEG data and I am searching a way to visualize the sEEG electrodes on MRI. I have the pre-operative MRI and the post-operative CT images (with electrodes visibles) and I would like to fuse them together and normalize them to the MNI brain atlas to pinpoint each contact exactly. Could you tell me if it can be done in Brainstorm and how I should proceed?

Thanks in advance.

Anaïs

[tmedani]

Hello Anaïs,

You can import the volumes to Brainstorm and co-register the modalities,
a good starting tutorial can be this one:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity
and
https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG

and fo the electrodes' position, you need to identify them from the volume one by one as explained in this section:

https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Edit_the_contacts_positions

Best,
Takfarinas

[Francois]

I would like to fuse them together

You can easily overlay CT+MRI, SEEG+CT, SEEG+MRI, SEEG+MRI+Atlas, but not MRI+CT+SEEG.
If you want to merge the SEEG contact positions for multiple subjects, this is not easy to do either.

and normalize them to the MNI brain atlas to pinpoint each contact exactly.

If you want the MNI coordinates of the SEEG contacts:

• In the MRI viewer, compute the MNI coordinates, preferentially using the Segment non-linear registration from SPM.
  https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates
• Right-click on the channel file > File > Export to file > Select for example the file format "EEG: ASCII: Name, XZY_MNI".

If you are expecting to see what region is associated to a contact in one of the available MNI-based parcellations:

• Right-click on the channel file > Display > MRI Viewer
• Right-click on MRI viewer figure > Set the atlas you want to use, and show it
• Move the cursor to navigate to the different contacts (the iEEG tab will take you easy only to the tip of each electrode)
  https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG#Volume_atlases
  https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#MNI_parcellations

During the late summer/fall, I will work on a solution to automatically export a table listing the parcels in all the atlases available for each SEEG contact.