Dear François,
we didn't use Brainstorm for modifying the fif file. We did that with a dedicated tool from MEGIN. This MEGIN tool only allow changing the transformation matrix, not the landmarks coordinates or the headshape points coordinates,
And we have only imported this modified fif file in Brainstorm afterwards. It is why I would like to check with you if during this import process, Brainstorm well read the new transformation matrix for positionning the head inside the helmet.
I didn't know that it was possible to change any value in a fif file with MNE. We will also try this.
Best regards
Etienne