[FieldTrip] EEG source reconstruction with template - elec file

Thu Jan 10 16:40:35 CET 2019

Hi Silvia,

have you tried the "interactive" method?
It lets you play around with the alignment.

Best,
Julian

On Thu, Jan 10, 2019 at 4:35 PM Silvia Formica <Silvia.Formica at ugent.be>
wrote:

> Dear Julian,
>
>
> thanks for your quick response!
>
> You are absolutely right, my problem was that I was not creating the elec
> file correctly as a struct with the fields chanpos, elecpos and label.
>
>
> I'm now facing another problem, though. I'm trying to use
> ft_electroderealign, but I can't seem to achieve a satisfying result. Here
> is what I am doing:
>
>
> cfg = [];
> cfg.method    = 'headshape';
> %     cfg.warp        =
> cfg.elec      = elec;
> cfg.headshape = vol.bnd(1);
> elec_new = ft_electroderealign(cfg);
>
>
> I then try to plot overlaid the skin surface as loaded
> from 'standard_skin_14038.vol' and the new electrode location but I get
> inconsistent results, the electrodes are always inside the head. I tried
> different warping methods without success. This is the closest I managed to
> get:
>
>
>
>
> Do you have any recommendation on how to better align the electrodes to
> the template?
>
>
> Thanks!
>
> Silvia
> ------------------------------
> *From:* fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Julian
> Keil <julian.keil at gmail.com>
> *Sent:* 10 January 2019 11:58
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] EEG source reconstruction with template - elec
> file
>
> Dear Silvia,
>
> how is the electrode location information from the BioSemi website not
> enough?
> Basically, you can create your own electrode definition by giving the
> labels and locations to a structure, e.g.
> elec.label{1} = 'Fp1';
> elec.chanpos(1,:) = [-27.0333934563814, 83.2002299946862,
> -3.05493522574547];
>
> or for all your electrodes in one go:
> elec.label = {'Fp1','AF7','AF3','F1','F5'};
> elec.chanpos = [-27.0333934563814, 83.2002299946862, -3.05493522574547;...
> -51.4205700085246, 70.7743429000555, -3.05493522574547;...
> -35.5608995849164, 76.2605952593987, 24.1279774030766;...
> -25.1195714566887, 62.1731210759014, 56.2665567427342;...
> -47.7073482911603, 58.9136687505812, 43.7676114900325];
>
> plot3(elec.chanpos(:,1),elec.chanpos(:,2),elec.chanpos(:,3),'*')
>
> or of course read them more elegantly from a text file ;-)
>
> It might be a good idea to double check the alignment with the template
> headmodel afterwards using ft_electroderealign
> You can then use this elec structure in all subsequent analyses.
>
> I hope that helps,
>
> Julian
>
> On Thu, Jan 10, 2019 at 10:59 AM Silvia Formica <Silvia.Formica at ugent.be>
> wrote:
>
>> Dear all,
>>
>>
>> I have a EEG dataset, collected with a Biosemi system with 64 channels. I
>> don't have the individual anatomical data for each participant, but I want
>> to perform source reconstruction to have at least a rough localization of
>> the activation I find.
>>
>>
>> Therefore, I intend to use the templates provided by fieldtrip. If I
>> understand correctly, independently of the source modelling technique that
>> I will choose to use, I need the following information:
>>
>>
>> 1) the *head model* : this would be the template '*standard_bem'*
>>
>>
>> 2) the *source model* : the template '*cortex_5124.surf.gii*'
>>
>>
>> 3) the *elec information* : this file should describe the spatial
>> configuration of the electrodes, but I can't retrieve it. I don't think any
>> of the templates available fits my data (they all have more than 64
>> channels and different configurations).
>>
>>
>> I tried to use the function ft_read_sens on my data but I get the
>> following error
>>
>>
>> elec    = ft_read_sens([data_filt5.mat'],'senstype','eeg');
>>
>>
>> Undefined function or variable 'lab'.
>>
>>
>> Error in channelposition (line 316)
>>
>> n   = size(lab,2);
>>
>>
>> Error in ft_datatype_sens (line 349)
>>
>>         [chanpos, chanori, lab] = channelposition(sens);
>>
>>
>> Error in ft_datatype_sens (line 158)
>>
>>     sens = ft_datatype_sens(sens, 'version', '2011v2');
>>
>>
>> Error in ft_read_sens (line 380)
>>
>> sens = ft_datatype_sens(sens);
>>
>>
>>
>> I found the cartesian coordinates of the electrodes on the Biosemi
>> website, with the x y z coordinates for each electrodes (as the little
>> example I'm giving below, but that's not enough.
>>
>>
>> Channel             x                                        y
>>                                 z
>> Fp1                 -27.0333934563814 83.2002299946862 -3.05493522574547
>> AF7                 -51.4205700085246 70.7743429000555 -3.05493522574547
>> AF3                 -35.5608995849164 76.2605952593987 24.1279774030766
>> F1                     -25.1195714566887 62.1731210759014
>> 56.2665567427342
>> F5                     -47.7073482911603 58.9136687505812
>> 43.7676114900325
>>
>> ...
>>                      ...                                        ...                                    ...
>>
>>
>>
>> *Do you have any suggestions on how to create a correct elec file fitting
>> my data?*
>>
>> Any help would be highly appreciated!
>>
>>
>> Silvia
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
> _______________________________________________
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> https://doi.org/10.1371/journal.pcbi.1002202
>
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