[FieldTrip] EEG Electrode / Volume Alignment Problem

smoratti at psi.ucm.es smoratti at psi.ucm.es
Thu Dec 19 16:35:47 CET 2013


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
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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