[FieldTrip] EEG Electrode / Volume Alignment Problem

[Julian Keil]

Dear all,

I have a problem of which I can't really find the source.

When I use the standard BEM-Model and the standard MRI together with our vendor-provided EEG electrode positions, I can nicely and reliably localize effects in source space (e.g. the visual N1, see attached source plot).

However, when I use an individual MRI (DICOM, imported via ft_read_mri, realigned interactively, resliced and segmented) to build a BEM-Model (Dipoli-Method), realign the electrodes to the new volume (using the interactive mode in ft_electroderealign) and subsequently build an individual lead field, the effect is shifted away from visual cortex and it appears as if the source and the MRI are misaligned.

The odd thing is, that if I leave the alignment step out, i.e. use the misaligned electrodes to build the lead field, the effect at least moves back to the visual cortex.

I hope the attached comparison between aligned and misaligned electrodes makes this a bit clearer.

Does anyone have an idea at which point this problem might occur?

Thanks a lot.

Julian


P.S.: Below are the basic steps I use:

%% 2.1. Build individual BEM-Model
% First Realign Volume. Set Nas LPA, RPA, and positive z-values

cfg=[];
cfg.method='interactive';
cfg.coordsys = 'ctf';

mri_r = ft_volumerealign(cfg,mri);

cfg=[];

mri_rs = ft_volumereslice(cfg,mri_r);

%% Segment the individual volume
cfg=[];
cfg.output={'brain' 'scalp' 'skull'};
cfg.brainsmooth = 5;
cfg.scalpsmooth = 5;
cfg.brainthreshold = .5;
cfg.scalpthreshold = .1;
mri_s = ft_volumesegment(cfg,mri_rs);

%% Create Headmodel
cfg=[];
cfg.interactive = 'no';
cfg.numvertices = 1000;

bnd_s = ft_prepare_mesh(cfg,mri_s);

cfg=[];
cfg.method='dipoli'; %
cfg.conductivity=[0.3300 0.0041 0.3300];

vol_s = ft_prepare_headmodel(cfg,bnd_s);

cfg = [];
cfg.mri            = mri_s;
grid               = ft_prepare_sourcemodel(cfg);

grid.inside = find(grid.brain==1)';
grid.outside = find(grid.brain==0)';
grid.pos = grid.pos*10; % Set right dimensions

%% Align Electrodes
cfg=[];
cfg.method='interactive';
cfg.elec=elec_128;
cfg.headshape=vol_s.bnd(1);

elec_new=ft_electroderealign(cfg);

%% 4. Make the Leadfield.
elec_new.type='eeg';
 
cfg=[];
cfg.channel = 1:126;
cfg.elec=elec_new;
cfg.vol=vol_s;
cfg.grid=grid;

lf = ft_prepare_leadfield(cfg);

%% BEAMFORMER 

cfg=[];
cfg.channel=1:126;
cfg.method='lcmv'; %Time-Domain-Beamformer
cfg.grid=lf;
cfg.vol=vol_s; 
cfg.elec=elec_new; 
cfg.reducerank  = 3; 
cfg.keepfilter='yes'; 

beamfilter = ft_sourceanalysis(cfg, dat4beam);

%% Keep the cfg, just add the filter.

cfg.grid.filter = beamfilter.avg.filter; % Now we'll use the filter defined above

lcmv_bl = ft_sourceanalysis(cfg, bl_dat);
lcmv_act = ft_sourceanalysis(cfg, act_dat);



********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

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