MRI registration process / Project EcoG electrodes on MNI/ICBM152 surface

Dear BST team,

I've got an EcoG data set and I intend to visualize all electrodes on the MNI cortex template, rather than on the subject's anatomy. I know that in order to do that, I need to transform the electrode coordinates from CFT to the MNI space. Under the MRI registration process I found what I think is a way to do it using the user interface.

However, I've noitice that this transformation works well for EcoG grids, but not so well for stips. When I compare electrodes in the subject anatomy and in the MNI space, I also notice that the accuracy of the transformation varies from subject to subject. Is there a reason for this? am I wrongly assuming this is a transformation from CTF to MNI coordinates? I would really appreciate any suggestion on whether this is the right or wrong thing to do.


The menu you are using is named "Project electrodes on surface". Within one given anatomy, it projects all the electrode contacts onto a triangular surface available in the subject anatomy (ALL of them, including strips). For ECOG, this menu is useful to project the contacts on the inner skull surface. But this does not perform any change of coordinate system (subject space <> MNI space). You should not use it to project the subject-space contacts onto the MNI-space skull.

We haven't implemented yet a menu to project easily a channel file from subject space to MNI space. It is not very complicated to do, but we have to set up a correct group analysis workflow for iEEG with this feature, which we will probably work on in the next few years.

For the moment, the only possibility to convert electrodes positions is to do it manually, with the conversion functions illustrated here:

If you are not familiar with Brainstorm scripting, you may need to start with this:
Tutorials/Scripting - Brainstorm

If you haven't followed this tutorial yet, I recommend you start by following it:
Tutorials/ECoG - Brainstorm

Thanks for the response Francois. So, in the function cs_convert, is the sMri input the subject's pre-processed MRI or the ICBM152 MRI template?

% CS_CONVERT: Convert 3D points between coordinates systems.
% USAGE: P = cs_convert(sMri, src, dest, P)
% Transf = cs_convert(sMri, src, dest)
% - sMri : Brainstorm MRI structure
% - src : Current coordinate system {'voxel','mri','scs','mni','world'}
% - dest : Target coordinate system {'voxel','mri','scs','mni','world'}
% - P : a Nx3 matrix of point coordinates to convert

So, in the function cs_convert, is the sMri input the subject's pre-processed MRI or the ICBM152 MRI template?

The first MRI imported in the anatomy folder in which you are working. If you want to convert surface or sensor coordinates for a specific subject: then the first MRI for this subject.