Here too, I have things to fix. I will try to find a way to always return MNI coordinates, even outside the head, possibly by using the linear MNI registration instead.
I will work on this soon, but it should not impact what you are trying to do now.
This fix is now available: Bugfix: Capture errors with missing MNI definition in CAT12 normaliza… · brainstorm-tools/brainstorm3@36c16f4 · GitHub
Is there a way to do this last step using Matlab commands?
See my previous post: Command line history - #4 by Francois