[FieldTrip] EEG Electrode / Volume Alignment Problem
smoratti at psi.ucm.es
smoratti at psi.ucm.es
Thu Dec 19 20:44:35 CET 2013
I thought of changing the dat4beam.elec to newelec. Does this help?
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 17:08, Julian Keil escribió:
> 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
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
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