[FieldTrip] EEG Electrode / Volume Alignment Problem

[Julian Keil]

Hi Stephan,

thanks for your quick reply.

If I change the cfg.elec definition in the call to the beamformer, the source projection follows the electrodes, i.e. when I use the misaligned electrodes, the source is in the visual cortex, and if I use the aligned electrodes, the source is left temporal.

If I leave the info for cfg.elec out, ft_sourceanalysis takes the electrode info from the lead field.

Am I maybe missing some step during the call to ft_prepare_leadfield? Maybe some rotation of the volume or something like this?

Thanks a lot once more.

Julian

Am 19.12.2013 um 16:35 schrieb smoratti at psi.ucm.es:

> 
> hmm… in theory every thing should be fine as the lead field is calculated with aligned electrodes to bnd_s. However, try to change the electrode positions as well in dat4beam. Does this help?
> 
> best,
> 
> Stephan
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> El 19/12/2013, a las 15:38, Julian Keil escribió:
> 
>> 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
>> <EEG_Vol_Alignment.pdf>
>> <N1_standard_brain.png>
>> 
>> 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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