[FieldTrip] Question regarding nonparametric testing for coherence differences

[Hwee Ling Lee]

Dear all and Prof Maris,

I'm re-posting this question again, as I didn't get any replies previously.

I’m interested to investigate if there are any differences in phase
synchronization in resting state data at timepoint 2 versus timepoint 1.
The EEG data was collected using 64 EEG channels, resting state, eyes
opened and eyes closed. I’ve arbitrarily segmented the resting state data
into epochs of 2s each, and the epochs with artifacts are excluded
completely from further analyses. I then performed mtmfft to get the
fourier representation of the data, extracted the coherence, and compared
the coherence difference of timepoint 2 versus timepoint 1 of all channels
paired with all other channels.

I figured that if I extract the connectivity analyses without specifying
the channelcmb, I get a 'chan_chan_freq' dimord variable that would allow
me to perform cluster-based statistical analyses. I get an output with
‘chan_chan’ dimord variable. However, I was not 100% sure that this is
correct, hence, I’ve inserted my code (see below). It’ll be great if you
could tell me if what I’m doing makes any sense at all. Also, I don’t know
how I can plot the results to see if it make any sense at all.

Also, I checked the values obtained from when I specified "cfg.channelcmb"
and when I did not specify "cfg.channelcmb", I noticed that the values were
somehow different. I would assume that the values to be similar, although
I'm not sure why they would have differences in the values obtained from
specifying "cfg.channelcmb".

This is my code that I've used thus far:

for sub = 1:5

    cfg                 = [];

    cfg.output          = 'fourier';

    cfg.channel         = {'all'};

    cfg.method          = 'mtmfft';

    cfg.keeptrials      = 'yes';

    cfg.tapsmofrq       = 5;

       cfg.foilim          = [0 100];

    cfg.taper           = 'dpss';

    % find the index for the c200 condition

   pre_c200_idx = find(data5.trialinfo == 201);

    cfg.trials          = pre_c200_idx;

    HLF_pre_c200         = ft_freqanalysis(cfg, data5);

post_c200_idx = find(data5.trialinfo == 200);

    cfg.trials          = post_c200_idx;

    HLF_post_c200         = ft_freqanalysis(cfg, data5);



cfg                 = [];

    cfg.keeptrials      = 'no';

    cfg.channel         = {'all'};

    cfg.removemean      = 'yes';

    cfg.method           = 'coh';

    HLF_pre_c200coh{sub}      = ft_connectivityanalysis(cfg, HLF_pre_c200);

    HLF_post_c200coh{sub}      = ft_connectivityanalysis(cfg,
HLF_post_c200);

end



load('D:\Hweeling_Programs\fieldtrip-20140330\template\layout\easycapM11.mat');

cfg_neighb.method = 'template';

cfg_neighb.layout = lay;

cfg_neighb.channel = 'all';

neighbours = ft_prepare_neighbours(cfg_neighb, sub_HLF_pre_c200coh{1});



cfg = [];

cfg.layout = lay;

cfg.neighbours = neighbours;

cfg.channel = 'all';

cfg.channelcmb = {cfg.channel, cfg.channel};

cfg.latency = 'all';

cfg.avgovertime = 'no';

cfg.avgoverchan = 'no';

cfg.parameter = 'cohspctrm';

cfg.method = 'montecarlo';

cfg.statistic = 'depsamplesT';

cfg.correctm = 'cluster';

cfg.tail = 0;

% cfg.clustertail = 0;

cfg.alpha = 0.05/8; % to correct for multiple comparisons across 8
frequency bands.

cfg.numrandomization = 10000;

cfg.ivar = 2;

cfg.uvar = 1;



% design matrices

clear design;

design(1,:) = [1:5, 1:5];

design(2,:) = [ones(1,5), ones(1,5) * 2];

cfg.design = design;

% for theta band

cfg.avgoverfreq = 'yes';

cfg.frequency = [4 8]; % I also performed the statistics for delta (2-4),
alpha (8-10.5), alpha (10.5-13), beta (13-20), beta (20-30), gamma (30-40),
and gamma (40-100).

[diffc200_theta_stat] = ft_freqstatistics(cfg, sub_HLF_post_c200coh{:},
sub_HLF_pre_c200coh{:});


When I tried to plot the results, I used this code:

cfg = [];

cfg.channel = 'all';

cfg.layout = 'lay';

cfg.zlim = [-1 1];

cfg.alpha = 0.05;

cfg.refchannel = 'all';

ft_clusterplot(cfg, diffc200_theta_stat);

However, I was not sure how I could plot the results. I get an error
message from Fieldtrip when using ft_clusterplot:

Error using topoplot_common (line 366)

no reference channel is specified

Error in ft_topoplotTFR (line 192)

[cfg] = topoplot_common(cfg, varargin{:});

Error in ft_clusterplot (line 372)

      ft_topoplotTFR(cfgtopo, stat);



According to your paper in 2007, the topoplot of the results were masked by
the spatio-spectral pattern of the significant clusters. I don't know how
to do this, and I would really appreciate if you can show me how to make
such a plot.

Thank you very much.

Kind regards,

Hweeling
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20140824/0fbff11d/attachment-0001.html>