[FieldTrip] ft_connectivityanalysis for one long trial

[Julien Catanese]

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*
*tel lab : +1 (519) 888 4567 ext 31354*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20140122/7febf41d/attachment-0001.html>