[FieldTrip] mne vs lcmv methods

[Magyari, Lilla]

Hi Beth,

I do not know how lcmv beamforming is implemented in FieldTrip, and I 
haven't used it before. But I did use the mne method for 
sourcelocalization in FieldTrip, so may I can answer some of your 
questions partially. But if someone is more expert in this area, 
comments are appreciated.

Belluscio, Beth (NIH/NINDS) [E] wrote:
> Hi fellow Fieldtripers-
> 
>   I am learning about the pros & cons of different methods for source 
> localization.  For some of my data sets, I want to localize evoked 
> activity (ERFs).  In one of them, I anticipated a single unilateral 
> primary site of activation and MNE worked very nicely for this.  In the 
> second, I am using auditory stimuli and therefore anticipated 
> bilaterally synchronous activity.  As was to be expected, (I think) MNE 
> gave a single site of activity near the midline.  I tried a parallel 
> approach, but specifying lcmv as the method for ft_sourceanalysis as 
> follows:
> 
>  
> 
> cfg = [];
> 
> cfg.method = 'lcmv';
> 
> cfg.grid = leadfield_02_stim1;
> 
> cfg.vol = vol;
> 
> cfg.lambda = 1e8;
> 
> cfg.checksize = inf;   %I’ve been inserting this and the next line 
> because I’ve gotten error messages about the size.  This didn’t happen 
> before, but these lines avoid the problem
> 
> cfg.checkconfig ='loose';
> 
> source3CB24_02_stim1 = ft_sourceanalysis(cfg, tlkCB24_02_stim1)
> 
>  
> 
> The output has a time dimension 1x601, and a pos dimension of 8196x3 
> dimension, but the avg.pow is only 1x8196.  I interpret this to mean 
> that the analysis averaged the power over some time interval instead of 
> computing the power in each leadfield position for each time point.  
> When I use the mne method, the output is clearly power for each time 
> point, and produces a beautiful movie, as indicated in the tutorial. 
> 
>  
> 
> My questions about the lcmv technique are:
> 
> 1.       Is there a fundamental difference between the lcmv approach and 
> the mne approach whereby it cannot compute the power at each time point, 
> but only gives a single average value for a time period?

As far as I know, the mne approach (compared to other methods, like 
beamforming) is favored for calculating source estimates of evoked 
activity over time. Therefore, I am not surprised that the lcmv is not 
doing the computation over time.
I found this a useful reading about the differences between beamforming 
and mne:

Jensen, O., Hesse, C., 2010, Estimating distributed representation of 
evoked responses and oscillatory brain activity, In: MEG: An 
Introduction to Methods, ed. by Hansen, P., Kringelbach, M., Salmelin, 
R., doi:10.1093/acprof:oso/9780195307238.001.0001

> 
> 2.       If so, how do I specify the time interval of interest (ie that 
> containing the main peak of the ERF) in ft_sourceanalysis?

I would use ft_redefinetrial. This function can select only a segment of 
  your trials.

> 3.       I thought one advantage of either MNE or LCMV was that I could 
> indicate my a priori hypothesis of the anticipated localization of the 
> source activity.  Do I do this with cfg.grid?  Is there a way to 
> indicate the number of anticipated dipoles?

A dipole model presupposes indeed that the activation is coming from a 
small area or from multiple separate small areas, while the mne and the 
beamforming approach are providing a distributed representation of the 
neural activity. The minimum "a priori" assumption is that the 
underlying activation is coming from the brain. The brain volume is 
discretized onto a 3-dimensional grid (this is the cfg.grid). And the 
current is estimated at these grid locations. So, in this sense, yes, 
these grid points are your dipoles. Typically, you specify  more 
thousands of these points.

I hope this helps.

Lilla Magyari


>  
> 
> Thanks in advance for your help-
> 
> Beth.
> 
>  
> 
> Beth Belluscio MD-PhD
> 
> Clinical Fellow
> 
> Human Motor Control Section
> 
> NINDS, NIH
> 
> 301-402-3495
> 
>  
> 
> 
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> 
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