beamformer on yokogawa data, grad.tra structure

[Robert Oostenveld]

Hi Sangi

On 9 Apr 2010, at 18:29, Sangita Dandekar wrote:
> Thanks for the below reply!   I was wondering if you or anyone
> familiar with the yokogawa MEG system
> could verify that we are using an appropriate grad.tra matrix and
> then subsequently determining the channel leadfield
> from grad.tra correctly.   Currently, we are using the generic
> definition for the grad.tra matrix from the yokogawa2grad.m
> file in the private fieldtrip directory:
>
> % Define the pair of 1st and 2nd coils for each gradiometer
> grad.tra = repmat(diag(ones(1,size(grad.pnt,1)/2),0),1,2);
>
> % Make the matrix sparse to speed up the multiplication in the forward
> % computation with the coil-leadfield matrix to get the channel
> leadfield
> grad.tra = sparse(grad.tra);
>
> Each of our channels is an axial gradiometer with two coils so I
> think that the above definition should be fine, but
> just wanted to check to be sure.

To check you could do the following

figure
hold on
axis vis3d
for i=1:160
   coils = find(grad.tra(i,:));
   coil1 = coils(1);
   coil2 = coils(2);
   plot3(grad.pnt(coil1,1), grad.pnt(coil1,2), grad.pnt(coil1,3), 'b.');
   plot3(grad.pnt(coil2,1), grad.pnt(coil2,2), grad.pnt(coil2,3), 'r.');
   disp('press return to continue')
   pause
end

which will visualise all coil pairs.


> One possibly complicating factor is that MEG160, the software that
> we use for data collection with the yokogawa system, has a list of
> 'calibration weights' for each gradiometer that are determined at
> each sensor tuning prior to data collection.  There is one calibration
> weight determined per channel (or 1 weight for every pair of
> coils).  Do these calibration weights need to be accounted for when
> determining grad.tra or the channel leadfield?

no the calibration weights are used when reading in the data from disk
into memory. In the forward computation (and inverse computation) they
should not be used.


best,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.