Hello,
I’m sorry for the response delay.
I cannot really tell what is going wrong with the alignment without looking into details at all the code and the files. Those issues with the transformations between coordinate systems are so difficult to understand…
I may have a much simpler solution to offer.
It looks like you have the position of the nasion placed in your file. Could you also mark two additional points to identify the left and right ears (LPA and RPA)?
The points we recommend using are described on this page:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems
If you have an electrodes file with those three landmarks (NAS/LPA/RPA), Brainstorm will automatically calculate the appropriate transformation to align the electrodes positions on the MRI.
The beginning (or end) of your text file could look like this:
Nasion 9.592 0.083 -1.885
LPA -0.474 6.819 0.628
RPA -0.960 -6.723 0.164
E1 4.335 3.089 12.941
E2 2.689 3.027 13.882
If you cannot set freely the name of the landmarks, you can use any of the equivalent labels below (not case-sensitive):
- NAS: nasion, nz, fidnas, fidnz
- LPA: pal, og, left, fidt9, leftear
- RPA: par, od, right, fidt10, rightear
Does this help?
Francois