[FieldTrip] question about virtual electrode MNI coordinates

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Wed Aug 7 14:52:32 CEST 2013

Dear Charidimos,

thanks very much for pointing to this, it is indeed an error in the 
appendix of the tutorial. cfg.grid.pos should be based on the 
subject-specific MRI or sourcemodel. So, correctly it should say that 
you need to load sourcemodel.mat (i.e. subject specific grid) and then 
use sourcemodel.pos(maxpowindx, :)
The rationale in principle is that the warped grid has the same size and 
is indexed the same as the original grid; that is why you can use the 
index variable obtained from the MNI-warped source reconstructed data. 
The virtual channel reconstruction should however still be done in 
whatever coordinate system the subject's anatomical data is in. I will 
update the appendix accordingly.


On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
> Hi there,
> I have a question regarding virtual electrodes: How can I double check 
> that the MNI coordinates that I enter are correctly interpreted?
> More specifically:
> I have followed the the extended beamforming tutorial in the 
> "Appendix" and have been able to transpose it to my data (I have 
> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
> about is the call to the LCMV beamformer.
> Here it is in my case ( I just want to get the voxel were the power is 
> max in the previous analysis):
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = volfcm;
> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.grad=senscm
> source_idx       = ft_sourceanalysis(cfg, tlock);
> My headmodel does not include MEG channel information so I need to 
> also define the cfg.grad parameter. What I don't understand is how 
> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
> the tutorial) can be correctly applied to the coordinates of the 
> headmodel and the channels since these 2 are not in MNI coordinates 
> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
> previous part of the tutorial this is (if I understand correctly) 
> accomplished because the leadfield used when calling ft_sourceanalysis 
> was created using and MNI-warped template. I don't see where the 
> equivalent part is when estimating the virtual electrode though.
> Any advice you may have would be much appreciated.
> Best,
> Haris
> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
> University of Minnesota Dept of Neuroscience and Brain Sciences Center
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130807/833d88b8/attachment-0002.html>

More information about the fieldtrip mailing list