[FieldTrip] help

Tue Nov 12 15:11:34 CET 2013

Hi Jan-Mathijs,

I had assumed that 'refchan' was a built in fieldtrip thing, that makes
more sense now! However, I'm unsure of whether I am supposed to be removing
the implicit reference, or the (in my case) linked mastoid references. I
ran the data using the cfg.runica.pca = N-1 parameters (I did it as N-2
actually, for the linked mastoid references) as described in the fieldtrip
FAQ, Peter, and you, but the data did come out a bit weird, and I would
prefer ICA over PCA, so I'll definitely try this as well and see if I get
results that make more sense to me.

On Tue, Nov 12, 2013 at 4:30 AM, Sendy Caffarra <s.caffarra at bcbl.eu> wrote:

> Thanks a lot.
> Now it works ;)
>
>
> Sendy
>
> ----- Original Message -----
> From: "jan-mathijs schoffelen" <jan.schoffelen at donders.ru.nl>
> To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> Sent: Tuesday, November 12, 2013 9:48:13 AM
> Subject: Re: [FieldTrip] help
>
>
> Hi Max,
>
>
> When you specify the channel to be left out, you have to name it according
> to how it's named in your data. I believe that the 'refchan' is only called
> like that for the purpose of the example.
> So, when you have a single reference channel, named
> 'thisisthenameofyourreferencechannel', you need to specify
> '-thisisthenameofmyreferencechannel', rather than '-refchan'. Sorry for
> exaggerating, but perhaps the silly name brings across the message more
> clearly. Note, that when you have applied a common average reference, you
> could at random remove a channel (not advisable). In that case I'd specify
> the dimensionality of your data space prior to calling
> ft_componentanalysis, as cfg.runica.pca = N-1 (N being the number of EEG
> channels).
>
>
> Best,
> Jan-Mathijs
>
>
>
> On Nov 11, 2013, at 4:46 PM, Max Cantor wrote:
>
>
>
> I'm having this issue as well, only with EEG data, and at resamplefs =
> 150. I've added '-refchan' to my cfg.channel for ft_componentanalysis, and
> also set path for EEGlab toolbox, but the issue persists. Any help would be
> greatly appreciated.
>
>
> Thank you,
> Max
>
>
>
> On Fri, Nov 8, 2013 at 5:14 AM, Stephen Whitmarsh <
> stephen.whitmarsh at gmail.com > wrote:
>
>
>
> Hi Sendy, JM,
>
>
> In addition, that error also happens (or used to, at least) when you have
> not selected MEG as channels, therefor applying ICA e.g. also on your EOG
> channels etc. as well.
>
>
> Cheers,
> Stephen
>
>
>
>
>
>
>
>
>
> On 8 November 2013 11:08, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl > wrote:
>
>
>
>
>
>
> Hi Sendy,
>
>
> You may want to have a look at the following link:
>
>
>
> http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers?s[]=component
>
>
> I assume that your data has been passed through the MaxFilter, which
> massively reduces the rank of your data, causing the ICA algorithm to spit
> out complex valued numbers.
> You need to reduce the rank of your data prior to running the component
> decomposition, to be less that then true rank in your data.
>
>
> Best
> Jan-Mathijs
>
>
>
>
> On Nov 8, 2013, at 10:47 AM, Sendy Caffarra wrote:
>
>
>
> Hi,
>
>
> I'm using Fieldtrip to analyze my Meg data.
> Actually, I'm trying to reject ocular artifacts by using ICA.
> I decreased the sample rate to 300 and I performed the ICA analysis as
> following:
>
> cfg = [];
> cfg.resamplefs = 300;
> cfg.detrend = 'no';
> data_1_rspl = ft_resampledata(cfg, data_1);
> %ICA
> cfg = [];
> cfg.method = 'runica';
> comp = ft_componentanalysis(cfg, data_1_rspl);
>
>
> It worked, but now when I try to visualize the different ICA components
> using:
>
> cfg = [];
> cfg.layout = 'neuromag306mag.lay'; % specify the layout file that should
> be used for plotting
> cfg.viewmode = 'component';
> ft_databrowser(cfg, comp);
>
> I can see how the waves look like, but I cannot see the topographic
> distribution of them.
>
> And Matlab gives me this error:
>
> ??? Error using ==> surf at 78
> X, Y, Z, and C cannot be complex.
>
> Error in ==> ft_plot_topo at 251
> h = surf(Xi-deltax/2,Yi-deltay/2,zeros(size(Zi)), Zi, 'EdgeColor', 'none',
> 'FaceColor',
> shading);
>
> Error in ==> ft_databrowser>redraw_cb at 1850
> ft_plot_topo(chanx, chany, chanz, 'mask', ...
>
> Error in ==> ft_databrowser at 671
> redraw_cb(h);
>
>
> Could you help me in solving this problem?
> I also downloaded the latest version of fieldtrip but it still does not
> work.
>
> Thanks for your help.
>
> Sendy
>
>
> Sendy Caffarra
> Postdoctoral researcher BCBL
> www.bcbl.eu
>
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>
>
>
>
>
>
>
>
>
>
> Jan-Mathijs Schoffelen, MD PhD
>
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
>
> http://www.hettaligebrein.nl
>
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>
>
>
>
>
>
>
>
>
> Jan-Mathijs Schoffelen, MD PhD
>
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
>
> http://www.hettaligebrein.nl
>
> _______________________________________________
> fieldtrip mailing list
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