[FieldTrip] question about virtual electrode MNI coordinates

[Elisa Carrus]

Hi all,

 From the previous email it seems that I'm doing something wrong then. I 
have previously used the MNI-aligned subject grid (warped template) for 
the positions, hence I didn't encounter any problem. However, this seems 
to be wrong, as Jorn suggested. The question is the following:

The sourcediff.avg.pow is produced using the warped MNI template, 
therefore the grid positions and indexes will be different from the 
subject-specific MRI. Specifically in my case, the warped template has 
11000 x 3 pos, whereas the subject-specific has 2652 x 3.
My question is, when I therefore index the maxpos using:

[maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
exceeds the matrix dimensions of the subject-specific MRI (2652).

Which step am I missing?

Thanks for your help in advance,
Elisa






On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
> 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.
>
> Best,
> Jörn
>
> 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
>>
>>
>>
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>
>
> -- 
> 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
>
> Contact:
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> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
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