SEEG channel MNI coordinates


I am trying around with stereo-EEG data in brainstorm; I already managed to import the data and events successfully from matlab.

Now, the coordinates of the SEEG channels are only available in the MNI coordinate system. I could also create a channel file and load this into brainstorm, and it correctly identifies the channels as SEEG channels. The channels, however, are now located somewhere outside the head. Until now, I could not find a way to tell brainstorm that the coordinates are in the MNI space, so it would know what to do with them. Do you have an idea?


Hi Martin,

I’m sorry, I haven’t had the time to write the import of channel files in MNI coordinates yet.
For now, you have to do the conversion MNI=>MRI manually. Some guidelines at the bottom of this page:

For using the MNI coordinates, you need first to compute the SPM MNI transformation:

There is no tutorial on how to manipulate the electrodes positions yet, but some information is available on the news page:


Okay, thanks, that is already very helpful!


Hello there, anything new on how to “tell” brainstorm where electrode positions are? something like "marking them in an mri?
best regards

Hi Jonas,

You can define the contact positions from the MRI viewer:

  1. Right-click on the channel file > Edit channel file > Set the type of the channels as SEEG. Close window to save.
  2. Right-click on the channel file > MRI registration > SEEG: Edit (MRI Viewer).
  3. In the MRI viewer, place the cursor where you want, right-click on the figure, place your contact

Alternatively, if you can set the contact positions in a different environment and export them to a text file, it can be simpler.
In this other environment (eg. neuronavigation system): add the position of the anatomical references NAS/LPA/RPA (use the same positions as set in the MRI viewer in the Brainstorm).
In Brainstorm, right-click on the channel file > Add EEG positions > Import from file, select the exported text file. If the points NAS/LPA/RPA are correctly set in the text file, the position of all the contacts should be converted automatically to Brainstorm coordinates.


thanks for the fast reply! working already! :wink:

FYI: We improved significantly the tools available in Brainstorm for processing and visualizing SEEG and ECOG data, including new options for volume coregistration. They are now documented in a new tutorial: