Hi @tmedani
Thank you for your answer.
Could you share the MRI?
I have rerun it on a Mac desktop with everything newest(Brainstorm, Simnibs). The result now looks good as the FEM mesh is perfectly aligned with T1. I presume the misalignment issue was related to the output from Simnibs version 2.1 Probably it is too old and I also needed to add an additional argument to the command in Brainstorm function process_fem_meshin order to run CAT12 within the external Simnibs process.
This error appear when you have the cortex nodes (source space) not aligned with the FEM mesh, and I think it's your case,
if you display the FEM mesh and the cortex, you can check it.A second possible issue is when you have holes in the FEM mesh, in this case, you need to re-mesh the head from the extracted surfaces using iso2mesh option (included in also within brainstorm)
[right click on FEM mesh=> extract surfaces,
then select all the extracted surfaces (hold the shift key)
=> right-click ==> generate FEM mesh => select Iso2mesh, and reduce the maxvol to 0.01 or less.This will generate a new FEM mesh free from possible mesh holes, then recompute the forward model DUNEuro.
The computer is still running, I will try to computer head model later with the correctly aligned FEM mesh. I'd let you know if the problem still exists. Your suggestion is much appriciated.