[FieldTrip] ft_clusterplot error?

[Jac Billington]

Dear Stephen,


Thank you for the useful reply, I've been doing some trouble shooting and it seems the output of  ft_freqstatistics doesn't seem to be reflecting my raw data. See "stat_discrepency.jpg" in dropbox link.


This plots condition 1 and 2 and the raw difference (as per your suggestion data_diff.powspctrm = data1.powspctrm - data2.powspctrm). I then plot stat.stat and the clusterplot output, clusterplot is representing my stat output.


In general I want to look at all channels, time 4-6seconds, for frequencies 8-12.  The latter 2 parameters I want averaged.


I noticed that the T-stat plot (of stat.stat) reports only one time and frequency. I presumed this was the average for display purposes (- double checked by plotting only that time and frequency in "stat_discrepency_onetimefreq.jpg" and it is different).


I think my design matrix is correct (following http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/). I have 28 trials in con1 and 25 in con2, my design matrix is 1x53 reflecting the trials for the two conditions. I don't think I need to specify anything further until I move on to group analysis (this is just a single subject).




The only other issue I can think of is in the parameter:

        cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, elec);


I create 'elec' by using ft_read_sens to read the preprocessing output from EEGlab.


        filenameA=strcat([det.subjects{s} '_postPreProICA_epoched_' det.epochs{1} '.set'])
        elec = ft_read_sens(filenameA)


Again, I'd be grateful for any pointers. My computation of ft_freqstatistics has not changed from the original post.

Thank you. Jac
<http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/>


https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0

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Subject: Re: [FieldTrip] ft_clusterplot error?
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Hi Jac,

I would start by plotting your (t)stats, and for simplicity doing that with
ft_singleplotER (cfg.param = 'stat') rather than ft_clusterplot.
Then try plotting the power-difference. This should not be more than a
subtraction of data_diff.powspctrm = data1.powspctrm - data2.powspctrm, .
No reshaping should be needed.
The problem is probably a mistake somewhere keeping track of
dimensions/latencies etc. which is tricky with clusters.
Also, make sure to clear your cfg before every function so you don't carry
the cfg of a previous function into the next. That will also help
readability and debugging.

HTH,
Stephen

________________________________
From: Jac Billington
Sent: 18 January 2019 18:07:04
To: fieldtrip at science.ru.nl
Subject: ft_clusterplot error?


Dear experts,


I've recently begun  using fieldtrip and have been following tutorials well. however, I have perhaps run into a problem with ft_clusterplot.


An example output is located in dropbox here: https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0


My negative cluster labels don't seem to be located in a cluster per se, or in regions with a greater raw effect. This seems at odds with tutorial examples and papers. Apologies if I'm missing something, but can this be correct?


I did have earlier errors ('  ft_error('unsupported dimord %s', dimord);') but I realised this was because dimensions of my stat.raweffect (64 5 200) were in conflict with collapsing time and frequency when running ft_freqstatistics. Reducing stat.raweefect to 64 1 solved this error, but I'm wondering if I have done something wrong.


My code is posted below and I'd happily be poited to some papers if I'm misunderstanding this.


Thank you in advance. Jac



  % load data  (from ft_freqanalysis)
        load(filename1);
        con1= freqScaling
        load(filename2);
        con2=freqScaling;

        %%%% run the stats:
        cfg = [];
        cfg.channel          =  'all';
        cfg.latency          = [4 6];
        cfg.frequency        = [8 12];
        cfg.method           = 'montecarlo';
        cfg.statistic        = 'ft_statfun_indepsamplesT';
        cfg.correctm         = 'cluster';
        cfg.clusteralpha     = 0.05;
        cfg.clusterstatistic = 'maxsum';
        cfg.minnbchan        = 2;
        cfg.tail             = 0;
        cfg.clustertail      = 0;
        cfg.alpha            = 0.025;
        cfg.numrandomization = 500;
        cfg.avgoverchan = 'no'
        cfg.avgovertime = 'yes'
        cfg.avgoverfreq = 'yes'
        % prepare_neighbours determines what sensors may form clusters
        cfg_neighb.method    = 'distance';
        cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, elec);

        design = zeros(1,size(con1.powspctrm,1) + size(con2.powspctrm,1));
        design(1,1:size(con1.powspctrm,1)) = 1;
        design(1,(size(con1.powspctrm,1)+1):(size(con1.powspctrm,1)+ size(con2.powspctrm,1))) = 2;
        cfg.design           = design;
        cfg.ivar             = 1;


        [stat] = ft_freqstatistics(cfg, con1, con2);



       cfg=[]
       cfg.keeptrials    = 'no'
       cfg.latency          = [4 6];
       cfg.frequency        = [8 12];
       con1 = ft_freqdescriptives(cfg, con1);
       con2  = ft_freqdescriptives(cfg, con2);

       %%%% resize powerspec to avoid dimord error. Collapse freq/ time
       con1rs=mean(con1.powspctrm,3)   %%% collapse time dim
       con2rs=mean(con2.powspctrm,3)   %%% collapse time dim
       con1rs=mean(con1rs,2)   %%% collapse freq
       con2rs=mean(con2rs,2)
       stat.raweffect = con1rs-con2rs

       cfg.alpha  = 0.025;
       cfg.zparam = 'raweffect';
       cfg.zlim   = [-1 3];
        cfg.layout = 'biosemi64.lay';
       cfg.subplotsize = ([1 1]);
        ft_clusterplot(cfg, stat);


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