[Simnibs-discuss] SimNIBS for EEG Source Reconstruction

Jesper Duemose Nielsen jesperdn at drcmr.dk
Tue Mar 23 12:04:42 CET 2021

Hi Jason

Sorry for the late reply.

 1. Yes, the leadfield is calculated for the x, y, and z components.
 2. Just omit the ground electrode. The electrodes in the forward
    solution should correspond to the electrodes in your data. Please be
    aware that due to the way the forward problem is solved with
    TDCSLEADFIELD (using reciprocity), you will need to multiply by -1
    when using it for EEG source analysis. Also, the number of channels
    in the leadfield is one less than in the cap file because one of
    them is used as reference during the simulation. You will need to
    add this yourself afterwards (all zeros). In the hdf5 file, the
    attributes 'reference_electrode' and 'electrode_names' in
    mesh_leadfield/leadfields/tdcs_leadfield should tell you which
    electrode was used as reference and the names of all the electrodes,
    respectively. Also, if you use an average reference in your inverse
    analysis, remember to also convert the forward solution to an
    average reference.
 3. We are currently working on SimNIBS 4.0 but it is not quite there
    yet. It will probably be a while before it is released but I do not
    know the exact plans. To my knowledge, we do not plan to implement
    inverse solvers in SimNIBS as there are plenty of great
    implementations available already, however, we do plan to allow
    people to interface with other packages. I believe we will support
    MNE-Python and perhaps FieldTrip. That way you should be able to
    integrate forward solutions from SimNIBS with inverse solvers from
    these software packages.

Let me know if anything is unclear.

Best wishes,


From: Jason Leung
Sent: March 10, 2021 11:49 AM
To: discuss at simnibs.org <discuss at simnibs.org>
Subject: SimNIBS for EEG Source Reconstruction


I am trying to use SimNIBS for EEG source reconstruction and I have a 
few questions.

   1.  I noticed that the leadfield matrix created with TDCSLEADFIELD 
that is stored in the hdf5 file has dimensions: [3 x number of nodes x 
number of EEG electrodes]. I was wondering what the first dimension of 3 
here represents. Is it the current density split into the X, Y, Z 
   2.  I'm trying to import my own EEG cap for the leadfield 
calculations. In the EEG cap CSV file, I noticed that reference 
electrode is labelled as 'ReferenceElectrode' as compared to other 
electrodes which are just labelled 'Electrode'. Is there another label 
for the ground electrode or should I just omit it from the CSV file?
   3.  I noticed Oula mentioned that SimNIBS 4.0 is available from this 
According to the abstract, SimNIBS 4.0 supports lead-field calculations, 
which allows the improved head modeling to be integrated into EEG source 
reconstruction algorithms. I was wondering where we could download and 
install version 4.0, since the latest one I can find is version 3.2. I'm 
also interested to know if this new version of SimNIBS come with EEG 
source inversion algorithms (i.e. MNE, LORETA) as well. Currently, I'm 
looking into how I can read the leadfield computed by TDCSLEADFIELD() 
into fieldtrip to do source inversion, but if SimNIBS 4.0 comes with 
support for these algorithms as well that would be very nice!

Thanks a lot for the amazing software package and I really appreciate 
your help!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20210323/1cc689a4/attachment.html>

More information about the Simnibs-discuss mailing list