Can't export cortex (to gifti) and electrode locations in the same space


I would like to export to matlab or to file the cortex (as a gifti) and SEEG channel locations aligned in the same space in order to plot activity in source and sensor space using custom plotting functions.

When visualizing the electrode locations in brainstorm, they are properly aligned on the cortex. However, when I export the cortex (either to file as a ‘.gii’ or directly to the matlab workspace) and plot with the electrodes (either from the file in anatomical coordinates that I originally imported in matlab, or the electrode locations exported from brainstorm -whether to file or to workspace-), they are misaligned. This is not only a matter of mm-cm conversion (problem persists after scaling)

In short, how can I apply to the electrodes that same transformation that is applied to the cortex when exporting from brainstorm?
Thanks a lot for your help,


All the 3D positions are saved in the Brainstorm database in the same coordinate system (SCS), vertices in the surface file and SEEG contact positions:

If you export to external file formats (eg. gifti), there are additional spatial transformations that might be applied. You can follow step by step the transformations applied for a specific file format in the corresponding export function. Example: