Import 3D scanner digitized electrode locations into BST


I have digitized the electrode locations (64 channels EEG) together with the fiducial points with a 3D camera, the same used in the Fieldtrip tutorial here:
I would like to import these electrode and fiducial locations into BST for accurate co-registration with the brain anatomy. Is there a simple way to do this either by importing the locations from the Fieldtrip format obtained following the above Fieldtrip tutorial, or by directly importing the 3D camera data into BST and digitizing the points there?




Hi Nicola,

For this you would need to export the fiducials and electrode locations (x,y,z) from FieldTrip. Multiple formats are supported in Brainstorm. An direct format would be a .csv file without header, and with four columns: Name, X, Y, Z.

In Functional view (iconStudyDBSubj), right-click on Subject > Import channel file.
Select file and EEG: ASCII: NAME,XYZ_MNI(.) type

For the moment Brainstorm do not support the data directly from the 3D camera.

Thank you Raymundo, I will try following your indications.



Dear Raymundo,

I tried following your indications. I ask one more feedback to be sure that what I am doing is correct.

Fieldtrip tutorial for registering the 3D electrode position consists of three main steps:

  • Localize the fiducials (NAS, LPA, RPA) on the head surface
  • Realign the mesh on the bases of the fiducials to CTF coordinates
  • Localise the electrode locations on this mesh

As far as I understand, BST also uses the CTF coordinate system, and BST definition looks identical to Fieldtrip one.

Following this logic, I directly imported the electrode locations computed from Fieldtrip into BST via import channel file > EEG: ASCII: Name,XYZ (,). Since the fiducials are integrated into the ctf coordinate system, as far as I understand there is no need to also import the fiducials in BST.

Is this procedure correct? It looks visually correct to me but I would like to be sure.

If this is not correct, how can I import the fiducials locations into BST? I did not manage to do that.

Thank you,



Hello @Raymundo.Cassani , I wonder whether you have missed my new message. Thanks,


Hi Nicola,

Registration between the CTF helmet (and the coils) and the Subject is done by having two pairs of fiducials: (i) fiducials in the subject anatomy, (ii) fiducials in the sensors coordinates (helmet). With the process that you describe, in FieldTrip the first set are the fiducials that are acquired by finding them in the head surface. And the second set are the fiducials for the CTF coordinates. With all this said

Yes, Brainstorm uses the Subject Coordinate System (SCS), which is defined as the CTF system.

In Brainstorm, the SCS is generated from the position of the fiducials on the subjects anatomy (this is the set (i) from the first paragraph above). As such, the coordinates exported from FieldTrip in the way described above, will be correct if-and-only-if the position of the first set of fiducials (i) are the same in Brainstorm and FieldTrip.