[FieldTrip] help

[Sendy Caffarra]

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 

_______________________________________________ 
fieldtrip mailing list 
fieldtrip at donders.ru.nl 
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 











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 


_______________________________________________ 
fieldtrip mailing list 
fieldtrip at donders.ru.nl 
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 

_______________________________________________ 
fieldtrip mailing list 
fieldtrip at donders.ru.nl 
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 










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