[FieldTrip] ft_connectivityanalysis for one long trial

[Julien Catanese]

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*
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