[FieldTrip] EEG Electrode / Volume Alignment Problem
Julian Keil
julian.keil at gmail.com
Fri Dec 20 10:07:42 CET 2013
Hi Stephan,
Ah, I forgot that the electrode definition is added to the EEG-structure.
Unfortunately, neither removing this nor setting all .elec-fields to the aligned elec_new helps.
Happy end-of-the-year wishes,
Julian
Am 19.12.2013 um 20:44 schrieb smoratti at psi.ucm.es:
>
> 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
>>>>
>>>> _______________________________________________
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>>>
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>>
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