[FieldTrip] help

[Max Cantor]

So we decided to remove both linked mastoid references for the ICA, and it
works just fine now. Thank you so much!


On Tue, Nov 12, 2013 at 9:11 AM, Max Cantor <mcantor at umich.edu> wrote:

> 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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>>
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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
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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>
>
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