[FieldTrip] Dipole time course

[jan-mathijs schoffelen]

Hi Mehmet,

I forward this to the mailing list, so that people can participate in  
the thread.

I do not fully understand where the orientation information in the vol  
comes from. The description of the volume conductor is namely a  
geometrical object, containing either a (set of) triangulated  
surface(s), to describe compartment boundaries, or the description of  
a (set of) sphere(s), with an origin and a radius.
The outcome of the dipolefitting algorithm gives you a field, called  
dip.mom, describing the dipole moment as a function of time. At each  
time point, the three numbers reflect the instantaneous orientation of  
the dipole. Since you are working with MEG, I assume that the  
orientation of this dipole is actually defined on a plane, because we  
routinely suppress the component with the most radial orientation from  
the leadfield. One way of reducing the dimension is to check whether  
there is a single dominant orientation over time. This can be achieved  
by doing a pca (or svd) of dip.mom. The ratio of the first two  
singular values specifies how well the dipole can be approximated as  
one having a fixed orientation. The left singular vectors give you the  
projection vectors, and thus specify the orientation. In other words  
[u,s,v] = svd(dip.mom). if s(1,1) >> s(2,2), one could justify to use  
u(:,1) as the 'orientation' of the corresponding dipole.

Best,

Jan-Mathijs





Begin forwarded message:

> From: Mehmet-Akif Coskun <mcoskun at mail.uh.edu>
> Date: March 31, 2011 8:57:30 AM GMT+02:00
> To: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> Subject: Dipole time course
>
> Hi Jan,
> Thanks for all your help. I am really close to get the dipole time  
> courses. Everything looks fine in terms of reading data,  
> preprocessing, creating headmodel and fitting a dipole. The last  
> part is to obtain a dipole time course.
>
> I actually read through the previous emails in discussion list and  
> followed the advices. I used the code below to obtain the leadfield  
> and then project the pinv'ed leadfield onto ERF to get the dipole  
> course. But the leadfield is 3D so i get 3 time courses.
> % prepare leadfield cfg=[]; cfg.grad= hdr.grad; cfg.vol=vol;  
> cfg.channel='MEG'; cfg.grid.pos=dipM50.dip.pos;
> [grid_ft_segment2]=ft_prepare_leadfield(cfg);
>
> In the email below, you suggested to an other user to multiply the  
> 3D leadfields with the orientation estimated by the dipole fit. I  
> checked the outcome of the dipole but there wasn't any orientation  
> information. However, i checked the vol structure which has the  
> orientation and multiply 3D leadfields with vol.ori and then project  
> 1d leadfield onto ERF. I got a nice looking time course. I just  
> wonder whether what i did is meaningful.
>
> Thanks
> Mehmet
>
> P.S= Below is your previous email
> I suspect that the 'orientation' onto which the pca projects the  
> dipoles is not optimal. Perhaps you might want to try the other way,  
> i.e. compute the leadfields in 1D, either by specifying something in  
> cfg.grid.mom (or ori, I keep forgetting) before calling  
> prepare_leadfield, or by postmultiplying the 3D leadfields with the  
> orientation as estimated by the dipole fit.

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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