Cannot Begin Electrode Localization

Discussions
1

Hello,

I have found several conflicting protocols for how to upload an MRI, CT, and then visualize EEG data and localize electrodes. To give a brief overview of where I am, and more importantly where I got stuck:

--I uploaded a subject's preop MRI in the file format .nii, with major success, and defined all fiducials.
--I uploaded a subject's sEEG CT scan as both a CT AND an MRI under the anatomy tab, and was able to overlay the two in both MRI viewer and the 3D viewer with success. I can see the electrodes in this fashion overlayed on the subject's MRI!
--I toggled over to the functional tab, and here is where I run into issues.

--I uploaded a raw EEG file (in a .edf file type), and it correctly entered the 276 total channels as "raw" data, but I cannot do MRI Registration>EEG Edit as some protocols suggest because it cannot find any 3D positions, MRI head points, or really anything useful. Even if I am able to put the channels onto my 3D head mask (I can't get the MRI to show up anymore under the functional tab), only 1 of my 276 channels is located in that view, and it is number 276 which is my PLETH channel and carries no important or relevant data.

How can I fix this?

2

The EDF files do not include the location of the sEEG.
You need to define the location of the sEEG from the CT as explained in this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/IeegContactLocalization

3

Okay, I will look over that link, but our CT scans are saved as sEEG_CT, meaning the two are already combined.

4

Check your files' format, how they are saved, and if Brainstorm supports them.

I don't know any standardized format that combines the sEEG and the CT in one file, and I'm not sure your format is supported by Brainstorm.

5

They are in DICOM format, and upon checking the link you sent me, here is where I get stuck--- * Right-click on the subject node > Import CT.
Select: tutorial_seeg_implantation/postCT.nii

  • Choose No for the NifTI Scaling. TODO-EXPLANATION
  • Choose Yes for the transformation for MRI orientation.
  • Choose CT2MRI and Yes for reslicing so that we can overlay the CT on the MRI

what file type am I supposed to choose when uploading? Any file type I use it tries to make my CT scan an MRI within Brainstorm. All CT files have been saved as both dicom files and nifti files.