SEEG electrodes and subject's anatomy are not alligned

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Hello,

The FreeSurfer surface coordinates are saved in FreeSurfer RAS coordinates (in voxels).
When imported into Brainstorm, they are converted first to Brainstorm MRI coordinates (in millimeters) at lines 141-148 in function in_tess.m:

% FreeSurfer RAS coord => MRI => millimeters
if ~isempty(sMri)
    mriSize = size(sMri.Cube) / 2;
    Vertices = bst_bsxfun(@plus, Vertices, mriSize / 1000);
    Vertices = bst_bsxfun(@times, Vertices, sMri.Voxsize);
end

Then are converted from Brainstorm MRI coordinates to Brainstorm SCS coordinates at line 193 in function in_tess.m:

TessMat(iTess).Vertices = cs_convert(sMri, 'mri', 'scs', TessMat(iTess).Vertices);

All the coordinates systems used in Brainstorm are documented here:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems

Does this help?
Francois