Hello,
Brainstorm re-writes everything it imports in the Brainstorm/CTF head coordinate system.
The transformation applied to the surfaces in FreeSurfer segmentation folder is not saved anywhere and depends on the MRI volume.
The easiest would be for me to add an option in the import of the electrode locations to import FreeSurfer coordinates.
I was already planning to do it with MNI coordinates (in one or two weeks).
It would be easier if I an example: could you send me an example FreeSurfer folder + contacts positions?
(upload it somewhere, then click on my username on this forum to send me the link in a separate email)
Thanks,
Francois