[FieldTrip] Compute Time-Frequency Granger Causality with ft_connectivityanalysis

[Hähnke, Daniel]

Hi Laetitia,

could you provide the code that you used for the calculation of your input structure ‘freq’?

When I had a similar looking issue it was because I used a trial-resolved structure, whereas GC calculation seems to require trial-averaged data.

Best, Daniel

On 10.08.2016, at 11:01, laetitia.lalla at inserm.fr<mailto:laetitia.lalla at inserm.fr> wrote:


Hi Daniel,

Thanks a lot for your answer. I was using a version from last September. I downloaded the most recent version "fieldtrip-20160809" this morning and I still have the same issue... When I call ft_connectivity analysis, this message is displayed : "the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated ... MB" and then Matlab stays stuck... I terminate it myself and the error is still the same :

Operation terminated by user during ft_checkdata>fixcsd (line 1072)
In ft_checkdata (line 595)
    data = fixcsd(data, cmbrepresentation, channelcmb);

In ft_checkdata>fixcsd (line 1170)
  data       = ft_checkdata(data, 'cmbrepresentation', 'full');
In ft_checkdata (line 595)
    data = fixcsd(data, cmbrepresentation, channelcmb);
In ft_connectivityanalysis (line 416)
          data = ft_checkdata(data, 'cmbrepresentation', 'full');

Has anyone else encountered issues when trying to plot a Time-Frequency Map of the Granger causality with ft_connectivityanalysis ?

Thanks a lot for your help.

Best,

Laetitia



On 08-08-2016 11:51, Hähnke wrote:

Dear Laetitia,

I think I had this issue before and it was caused by a bug in the fieldtrip version I was using. What version are you using?

Best,

Daniel
--
Daniel Hähnke
PhD student

Technische Universität München
Institute of Neuroscience
Translational NeuroCognition Laboratory
Biedersteiner Straße 29, Bau 601
80802 Munich
Germany

Email: daniel.haehnke at tum.de<mailto:daniel.haehnke at tum.de>
Phone: +49 89 4140 3356

On 08.08.2016, at 11:36, laetitia.lalla at inserm.fr<mailto:laetitia.lalla at inserm.fr> wrote:

Hello fieldtrippers,
first of all, thanks a lot for this collaborative mailing list. It helped me a lot in the past and i hope you will be able to help me today !

I succesfully implemented the spectral granger causality thanks to this FieldTrip tutorial : http://www.fieldtriptoolbox.org/tutorial/connectivityextended. Now I'd like to compute a Time-Frequency Map of my granger causality. Hence, I used ft_freqanalysis with cfg.method  = 'mtmconvol' and cfg.output  = 'powandcsd' and the minimal code
>cfg=[];
>cfg.method='granger';
>granger=ft_connectivityanalysis(cfg, freq);
to compute the granger causality.
However, when I run this code, Matlab bugs and stays "busy" for a while until I terminate it, with the following error message :

Operation terminated by user during ft_checkdata>fixcsd (line 1255)

In ft_checkdata (line 797)
    data = fixcsd(data, cmbrepresentation, channelcmb);

In ft_checkdata>fixcsd (line 1351)
  data = ft_checkdata(data, 'cmbrepresentation', 'full');

In ft_checkdata (line 797)
    data = fixcsd(data, cmbrepresentation, channelcmb);

In ft_connectivityanalysis (line 392)
          data = ft_checkdata(data, 'cmbrepresentation', 'full');

I can see in the help of the function checkdata the following :  "cmbrepresentation  = sparse, full (applies to covariance and cross-spectral density)". But I don't really understand what "cmbrepresentation" do ... Maybe someone who had a similar problem in the past can help me ? I think I'm missing some optional arguments that I should add.

Thanks a lot for your help.

Regards,

Laetitia Lalla
PhD student in INMED, Marseille, France
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