[FieldTrip] Resting State EEG Connectivity

[Elene Beitia Loinaz]

Dear Eelke,

We are following the tutorial that you have send us but we want to
perform *ft_sourceparcellate
*before connectivity to group the centroide of the voxels into regions,
since we want to reduce the grid. Otherwise, computing the lines requieres
computationally big effort which causes MEMORY errors.

[image: image.png]

The problem cames because in our *source*, which is obtained from*
ft_sourceanalysis
,* the number of* source.pos *is really big and matlab does not work with
this. We have seen that if we increase the size of the grid when we create
the leadfield we do not have Memory problems, but we think that is not very
accurate. That is why we want to create before
*ft_connectivityanalysis *different
regions to perform connectivity analysis between them and do not have
computatioinal probems.

Thanks for your help.


Hau idatzi du Eelke Spaak (e.spaak at donders.ru.nl) erabiltzaileak (2019 mai.
8, az. (11:59)):

> Dear Elene,
>
> Have a look at ft_sourceparcelllate and the following tutorial,
> particularly the part about parcellation:
> http://www.fieldtriptoolbox.org/tutorial/networkanalysis/ .
>
> Cheers,
> Eelke
>
>
> On Wed, 8 May 2019 at 08:57, Elene Beitia Loinaz
> <elene.beitia at alumni.mondragon.edu> wrote:
> >
> > Dear all,
> >
> > Continuing with the connectivity issue, we have seen that the problem of
> memory come from the size of the leadfield`s grid used previously for
> source reconstruction and now for connectivity. The variable related with
> that grid is data.pos,  which was created in ft_prepareleadfield. This
> value contains the coordinates of the centroids' voxels, related with the
> grid. As this variable is too large, it supposes really high computational
> effort that matlab cannot handle.
> >
> > We want to cluster the data.pos voxels coordinates into different brain
> regions such as: temporal area, frontal field....
> >
> > Does anyone know how we can group those coordinates into regions in
> order to decrease the size of data.pos variable needed in
> ft_connectivityanalysis function?
> >
> > Thank you in advanced.
> >
> > Hau idatzi du Elene Beitia Loinaz (elene.beitia at alumni.mondragon.edu)
> erabiltzaileak (2019 mai. 7, ar. (11:11)):
> >>
> >> Hi Fieldtripers,
> >>
> >> We are trying to perform a conectivity analysis using source
> reconstructed data. We have seen that ft_connectivityanalysis can be
> calculated using the output of ft_freqanalysis or ft_sourceanalysis.
> Someone knows which are the benefits of using the results obtain in
> ft_sourceanalysis to perform the connectivity analysis?
> >>
> >> Furthemore, we have problems when we compute the choerence approach
> with the source reconstructed data.
> >>
> >> Our code:
> >>
> >> cfg           = [];
> >> cfg.method    = 'coh'
> >> coh           = ft_connectivityanalysis(cfg, beamformer);
> >>
> >> The error that we obtain is:
> >> Out of memory. Type "help memory" for your options.
> >>
> >> Error in univariate2bivariate (line 314)
> >>          data.crsspctrm = (transpose(mom)*conj(mom))./nrpt;
> >>
> >> Error in ft_connectivityanalysis (line 449)
> >> [data, powindx, hasrpt] = univariate2bivariate(data, 'mom',
> 'crsspctrm', dtype, 'cmb', cfg.refindx,'keeprpt', 0);
> >>
> >> This segment of code has been concluded following the tutorials below:
> >> http://www.fieldtriptoolbox.org/tutorial/networkanalysis/
> >> http://www.fieldtriptoolbox.org/tutorial/connectivity/
> >>
> http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-connectivity-demo/
> >>
> >> Thank you in advanced,
> >>
> >> Waiting for your answer.
> >
> > _______________________________________________
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> > 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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