[FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
Lucia Melloni
lmelloni at gmail.com
Fri May 3 14:48:01 CEST 2013
Hi Jörn,
I downloaded version 20130502 and ran both my code and the test code that
you had emailed. I get 1 and inf with both.
The freq input seems to be ok, so ist must be an issue with
ft_connectivityanalysis.
Lucia
--
Lucia.
On Fri, May 3, 2013 at 2:32 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:
> Dear Lucia,
>
> could you try whether the error persists with a recent version? If it
> does, could you go test whether this code gives the same error:
>
> *
> % ************* code starts here *
> *%dummy data
> cfg = [];
> cfg.ntrials = 500;
> cfg.triallength = 1;
> cfg.fsample = 200;
> cfg.nsignal = 3;
> cfg.method = 'ar';
> cfg.params(:,:,1) = [ 0.8 0 0;
> 0 0.9 0.5;
> 0.4 0 0.5];
> cfg.params(:,:,2) = [-0.5 0 0;
> 0 -0.8 0;
> 0 0 -0.2];
> cfg.noisecov = [0.3 0 0;
> 0 1 0;
> 0 0 0.2];
>
> data = ft_connectivitysimulation(cfg);
>
>
> % freqanalysis
> cfgf = [];
> cfgf.method = 'mtmfft';
> cfgf.output = 'fourier';
> cfgf.tapsmofrq = 2;
> freq = ft_freqanalysis(cfgf, data);
>
> % connectivityanalysis
> cfgc = [];
> cfgc.method = 'coh';
> c1 = ft_connectivityanalysis(cfgc, freq);
>
> c1.cohspctrm**
> % ************* code ends here
> *
> The code snippet above is part of our test suite for making sure that
> everything works fine. If it does work for you, but does not with your own
> data instead of simulated data, the error must be somewhere in your data,
> e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that it will
> all work fine if you use an updated version of FieldTrip.
>
> Best,
> Jörn
>
>
>
> On 5/3/2013 12:56 AM, Lucia Melloni wrote:
>
> Hi Jan-Mathijs,
> still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
> In ft_connectivity_corr at 87
> In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
> In ft_connectivity_corr at 89
> In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
> In ft_connectivity_corr at 106
> In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
> Lucia
>
> --
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Lucia,
>>
>> The warnings indicate that you are dividing by zero. Are you sure that
>> your cfg is correct?
>>
>> Please try
>>
>> cfg = [];
>> cfg.method = 'coh';
>> coh = ft_connectivityanalysis(cfg, freq);
>>
>> This should work.
>>
>> Best,
>> Jan-Mathijs
>>
>> On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>>
>> Hi jan-mathijs
>>
>> Unfortunately I get the same result whether or not I remove the mean.
>> Best,
>> -- Lucía
>>
>> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
>> jan.schoffelen at donders.ru.nl> wrote:
>>
>> Hi Lucia,
>>
>> Could you remove cfg.removemean = 'yes' and try again?
>>
>> Best,
>>
>> Jan-Mathijs
>>
>> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>
>> Hi!
>> I am trying to calculate coherence using ft_connectivityanalysis, but
>> I am getting only ones and infinity as output in cohspctrm with all of
>> my data sets.
>>
>> I first run ft_freqanalysis with
>> cfg.method = 'mtmfft';
>> cfg.taper = 'dpss';
>> cfg.output = 'fourier';
>> cfg.foilim = [1 45];
>> cfg.tapsmofrq = 1;
>> cfg.keeptrials = 'yes';
>> cfg.keeptapers = 'yes';
>> freq = ft_freqanalysis(cfg, data);
>>
>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>> does not seem to make a difference for my problem later on. The
>> spectra look absolutely fine.
>>
>> I then run ft_connectivityanalysis with
>> cfg.method = 'coh';
>> cfg.removemean= 'yes';
>> cfg.trials = 'all';
>> cfg.feedback = 'yes';
>> cfg.complex = 'abs';
>> coh = ft_connectivityanalysis(cfg, freq);
>>
>> The cohspctrm looks like this:
>> val(:,:,1,1) =
>>
>> 1 Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
>> Inf Inf Inf (etc.)
>>
>> I get the following warning during ft_connectivityanalysis
>>
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 103
>>
>> In ft_connectivityanalysis at 524
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 104
>>
>> In ft_connectivityanalysis at 524
>>
>> The same happens if I try to calculate PLV through
>> ft_connectivityanalysis.
>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>> Windows 7 (64bit).
>>
>> Any advice?
>> Thanks!
>> Lucia
>> _______________________________________________
>> 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
>>
>>
>> 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 listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel: +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
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