Dear Francois,
after some playing around with Brainstorm we were able to reach a quasi-perfect alignment (see attached figure). We are only ~1cm far from the real positions. As you can see F1 represent the Nasion coordinates picked in 3DSlicer. We saved that position in the same channel file were we stored the other channel positions. After importing the channel file, brainstorm shows the F1 few mm backwards and probably also it misalign along Z-axis.
We applied exactly the same codes you applied in cs_convert + translation (mri.size/2).
Have any of you working on SEEG experienced the same problem?
All the best,
g.
