Hello,
I finally added this option to add explicitly coordinates in "world" coordinates:
https://github.com/brainstorm-tools/brainstorm3/commit/59c2b65a65f3a0a16c2c73b77806c900b8d46743
Link your SEEG recordings to your Brainstorm database, right-click on the channel file > Add EEG positions > Load from file > Select one of the EEG: ASCII formats ending with "_World" (N=Name), depending on the format of the file you have created from slicer.
This would work only if the positions are exported based on the transformation from the .nii file. I don't know if this is what slicer does.
If you still don't manage to import your files, please post some more information so we can help you better (screen captures showing what menus you are using, what does it look like in slicer, in Brainstorn, etc).