[FieldTrip] ft_connectivityanalysis for one long trial

[Лукоянов Максим]

Hi Julien,

I suppose you may to try to use cfg.keeptapers = 'yes' with
ft_freqanalysis. It's working for me.

Best,
Maxim Lukoyanov


2014-02-14 2:18 GMT+04:00 Julien Catanese <catanese.julien at gmail.com>:

> It works fine if I artificially slice the data into trials.
>
> (nb: MATLAB's mscohere() works fine without chopping into trials, so I was
> guessing it was also possible with the fieldtrip functions, but apparently
> not, sorry about that, not a big deal).
>
> Julien C
>
>
>
> On Wed, Jan 22, 2014 at 1:22 PM, Julien Catanese <
> catanese.julien at gmail.com> wrote:
>
>>
>> Hi dear FieldTrip community,
>>
>> I'm trying to get the coherence spectrum between 2 LFP signals (based on
>> the tutorial: "Analysis of sensor- and source-level connectivity").
>>
>> This is sleep data, so I have only one long "trial" generated with
>> ft_redefinetrial().
>>
>> I can run ft_freqanalysis() without problems, but both for 'mtmconvol'
>> and 'mtmfft' the next step, ft_connectivityanalysis(), fails:
>>
>> 1/ using 'mtmconvol':  the cohspctrum consists of all '1' (the same
>> happens when using 'fourier' instead of 'powandcsd')
>> 2/ using 'mtmfft': "Error using ft_connectivityplot (line 99) the data
>> should have a dimord of chan_chan_freq or chancmb_freq"
>>
>> How can I get a coherence spectrum for this data? Do I have to
>> artificially chop it up into say, 2-second "fake trials"?
>>
>> notice that MATLAB's mscohere() works fine on the same data (so data are
>> ok).
>>
>>
>>
>> More details below:
>>
>>  1/ using mtmconvol :
>>
>> %% starting point: loaded data
>>  data =
>>             hdr: [1x1 struct]
>>           label: {'LFP1'  'LFP2'}
>>            time: {[1x200000 double]}
>>           trial: {[2x200000 double]}
>>         fsample: 2000
>>             cfg: [1x1 struct]
>>      sampleinfo: [1 200000]
>>
>> %% make one long trial
>> cfg = [];
>> cfg.trl = [1 200000 0];
>> data_faketrl = ft_redefinetrial(cfg,data);
>>
>> %% do frequqency anlaysis
>>     cfg              = [];
>>     cfg.output       = 'powandcsd';
>>     cfg.method       = 'mtmconvol';
>>     cfg.taper        = 'hanning';
>>     cfg.foi          = 1:1:150;
>>     cfg.t_ftimwin    =  ones(size(cfg.foi)).*2; % 2-second window
>>     cfg.toi          =  0:1:10;
>>     cfg.keeptrials   = 'yes';
>>     cfg.channel      = {'LFP1', 'LFP2'};
>>     cfg.channelcmb   = {'LFP1', 'LFP2'};
>>
>> >> freq = ft_freqanalysis(cfg, data_faketrl)
>>
>> freq =
>>         label: {'LFP1'  'LFP2'}
>>         dimord: 'rpt_chan_freq_time'
>>           freq: [1x150 double]
>>           time: [0 1 2 3 4 5 6 7 8 9 10]
>>      powspctrm: [4-D double]
>>       labelcmb: {'LFP1'  'LFP2'}
>>      crsspctrm: [4-D double]
>>      cumtapcnt: [1x150 double]
>>            cfg: [1x1 struct]
>>
>> %% coherence spectrum has all ones
>> cfg           = [];
>> cfg.method    = 'coh';
>> coh           = ft_connectivityanalysis(cfg, freq);
>>
>>  coh =
>>
>>       labelcmb: {'LFP1'  'LFP2'}
>>         dimord: 'chan_freq_time'
>>      cohspctrm: [1x150x11 double]
>>           freq: [1x150 double]
>>           time: [0 1 2 3 4 5 6 7 8 9 10]
>>            dof: 150
>>            cfg: [1x1 struct]
>>
>> % coh.cohspctrm(:,:,2:end) is all ones --> fail
>>
>> 2/ using mtmfft:
>> %%
>> cfg              = [];
>> cfg.output       = 'powandcsd'
>> cfg.method       = 'mtmfft';
>> cfg.taper        = 'hanning';
>> cfg.foi          = 1:1:150;
>> cfg.channel      = {'LFP1', 'LFP2'};
>> cfg.channelcmb   = {'LFP1', 'LFP2'};
>>
>> >> freq = ft_freqanalysis(cfg, data_faketrl)
>>
>> freq =
>>
>>         label: {'LFP1'  'LFP2'}
>>        dimord: 'rpt_chan_freq'
>>          freq: [1x150 double]
>>     powspctrm: [1x2x150 double]
>>      labelcmb: {'LFP1'  'LFP2'}
>>     crsspctrm: [1x1x150 double]
>>     cumsumcnt: 200000
>>     cumtapcnt: 1
>>           cfg: [1x1 struct]
>>
>> %% coherence spectrum fails:
>> cfg           = [];
>> cfg.parameter = 'cohspctrm';
>> cfg.channelcmb   = {'LFP1', 'LFP2'};
>>
>> >> ft_connectivityplot(cfg,  coh);
>>
>> Error using ft_connectivityplot (line 99)
>> the data should have a dimord of chan_chan_freq or chancmb_freq
>>
>> coh =
>>      labelcmb: {'LFP1'  'LFP2'}
>>        dimord: 'chan_freq'
>>     cohspctrm: [1x150 double]
>>          freq: [1x150 double]
>>           dof: 1
>>           cfg: [1x1 struct]
>>
>> >> unique([coh.cohspctrm(:)])
>>
>> ans =
>>
>>    1.000000000000000
>>    1.000000000000000
>>    1.000000000000000
>>    1.000000000000000
>>    1.000000000000000
>>
>>
>> Thanks for your help,
>>
>> Julien C
>>
>> --
>>
>> *Dr. Julien Catanese*
>>
>> *VanderMeerLab post-doc.   University of Waterloo, Ontario, Canada. *
>> *cell : +1 (519) 781 7575 <%2B1%20%28519%29%20781%207575>*
>> *tel lab : +1 (519) 888 4567 ext 31354
>> <%2B1%20%28519%29%20888%204567%20ext%2031354>*
>>
>
>
>
> --
>
> *Dr. Julien Catanese*
>
> *VanderMeerLab post-doc.   University of Waterloo, Ontario, Canada.*
> *cell : +1 (519) 781 7575*
> *tel lab : +1 (519) 888 4567 ext 31354*
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20140214/062205ef/attachment-0002.html>