Problem with data from BESA

[Michael Wibral]

Hi Robert,

thank you very much for the quick reply. I noticed that I supplied
insufficient information. I actually switched on the electrode labels in
the display and the peaks sit at the wrong electrodes. I therefore
assume it is not a problem of the layout file (alone). I actually took
into account that the data look heavily distorted and tried to check
wether it is just a projection problem by playing around with different
scalings of elec.pnt (albeit this didn't seem to affect the plot??).
I should have also mentioned that I'm using version 20051113. However I
imported the electrode positions with read_fcdc_elec from the version
0.9.6 (there doesn't seem to be a read_fcdc_elec version supplied with
2005113..) - I hope this doesn't cause the trouble.
Meanwhile I also tried to use the elec1010.lay layout file which works
fine.However, in fieldtrip I find a negative peak between electrodes P5
P3 PO7 PO3 and a positive central one at CPz Cz (which has no
counterpart in BESA, so contourlines don't match exactly), whereas in
BESA a positive peak is found on CP4. This looks like an inversion of
signs, an inversion of left/right and a difference in the interpolation
algorithm.

Below you'll find the code I used (most of it is copied from the BESA
tfc sample page on the web site):

% this is the list of BESA datafiles in one condition
filename_AM = {
  'AA_AMU2M.mul'
  'AK_AMU2M.mul'
  'CB_AMU2M.mul'
  'HDR01_AMU2M.mul'
  'KRT28_AMU2M.mul'
  'KSN14_AMU2M.mul'
  'LM_AMU2M.mul'
  'MN_AMU2M.mul'
  'MW_AMU2M.mul'
  'MWA_AMU2M.mul'
  };

% this is the list of BESA datafiles in the other condition
filename_vAM = {
  'AA_vAMU2M.mul'
  'AK_vAMU2M.mul'
  'CB_vAMU2M.mul'
  'HDR01_vAMU2M.mul'
  'KRT28_vAMU2M.mul'
  'KSN14_vAMU2M.mul'
  'LM_vAMU2M.mul'
  'MN_vAMU2M.mul'
  'MW_vAMU2M.mul'
  'MWA_vAMU2M.mul'
  };

nsubj = length(filename_AM);

% collect all single subject data in a convenient cell-array
for i=1:nsubj
  AM{i} = besa2fieldtrip(filename_AM{i});
  vAM{i} = besa2fieldtrip(filename_vAM{i});
end

% load electrode configuration
elec= read_fcdc_elec('AA_AMU2M.sfp');
elec.pnt = 10.*elec.pnt; % scale, doesn't seem to affect the plotting ?

cfg = [];
cfg.keepindividual = 'yes';
AMdata = timelockgrandaverage(cfg, AM{:});
vAMdata = timelockgrandaverage(cfg, vAM{:});

DiffData=AMdata %create dummy structure to hold results of the
difference calculation
%calculate grand average difference
DiffData.individual=AMdata.individual-vAMdata.individual;
cfg = [];
DiffDataGA=timelockgrandaverage(cfg, DiffData);
%plot the differences
figure;
cfg=[];
plotdata1.elec=elec;
plotdata1.time=DiffDataGA.time;
plotdata1.label=DiffDataGA.label;
plotdata1.data2plot=DiffDataGA.avg;
cfg=[];
cfg.layout=elec;
cfg.showlabels   = 'yes'
cfg.zparam='data2plot';
cfg.colorbar='no';
cfg.xlim=[0.5595:0.001:0.5605]; % to zoom in on 560ms, as BESA only
gives data a timepoints
topoplotER(cfg,plotdata1);



Best Regards,
Michael



M. Wibral Dipl. Phys.
Max Planck Institute for Brain Research
Dept. Neurophysiology
Deutschordenstrasse 46
60528 Frankfurt am Main
Germany

Phone:       +49(0)69/6301-83849
                 +49(0)173/4966728
Fax:           +49(0)69/96769-327


Robert Oostenveld schrieb:

> Hi Micahel
>
>> I see in BESA (more like something differentiated / inverted from
>> the BESA maps - the foci are clearly shifted).
>
>
> The projection of the 3D electrode locations towards the 2D plane (in
> which the color-coded data has to be represented on screen or paper)
> might be quite different. Fieldtrip uses layout files in which you
> can specify the location of each sensor in the 2D plane (have a look
> at one of the *.lay files). If you do not specify a layout file, the
> 2D layout is constructed on the fly from the 3D electrode locations
> that are represented as NelecX3 matrix in data.elec.pnt.
>
> I suggest that you turn on the electrodes in topoplotER
> (cfg.showlabels option) and see whether that makes sense.
>
> If you are using standard labels of the extended 10-20 system in your
> EEG data, you can also try topoplotting with a predefined 2D layout,
> e.g.
>
> cfg = ...
> cfg.layout = 'elec1020.lay'  % or elec1010.lay
> topoplotER(cfg, avg)
>
>> Do I have to tell Fieldtrip somewhere that this is EEG data, so  that
>> it doesn't do the things it would when dealing with MEG  gradiometer
>> data?
>
>
> No, the topoplotting of EEG data and MEG data is done just the same.
>
>> Or is there something I have to do to let fieldtrip know that the
>> data are average reference data. I can't find anything in the
>> tutorials on this matter.
>
>
> No, referencing of EEG data does not influence the spatial
> topographical distribution. It might change the global color
> (depending on the coloraxis), but not the pattern. Re-referencing
> your data at one timepoint just subtract a constant value (the
> potential at the reference electrode) from all electrodes. A
> geographical map of the Himalayas would also look the same if you
> would express the height with respect to the foot of the mountain
> range instead of with respect to the sea level.
>
> best regards,
> Robert
>
> .
>

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