[FieldTrip] Error using ft_clusterplot (line 153)

[MUSTAFA YAVUZ]

Dear Bruno,

As far as I know, ft_clusterplot cannot handle the given data structure of
your stat output variable. You may consider using ft_multiplotTFR with the
mask created by the ft_freqstatistics by adding the mask to the struct data
you have for plotting.

For instance;
%% Prior to calling plot functions;
your_TFR_data_to_be_plotted.mask = your_stat_variable.mask
cfg = [];
cfg.layout = your_layout;
cfg.maskparameter = 'mask';
cfg.maskstyle = 'outline';
ft_multiplotTFR(cfg,your_TFR_data_to_be_plotted)


Hope I am not mistaken and it helps,
Best,
Mustafa

Bruno Mansur via fieldtrip <fieldtrip at science.ru.nl>, 1 Haz 2021 Sal, 17:35
tarihinde şunu yazdı:

> Dear fieldtrip list members,
>
> I'm trying to perform a *cluster based permutation test* on
> *time-frequency* data obtained from 'FT_FREQANALYSIS'.
>
> I execute the following command for it:
>
> % 2. Permutation test
>
> cfg = [];
> cfg.channel           = {'EEG'};
> cfg.latency            = [0 1.8];
> cfg.frequency        = 'all';% all frequencies from 2 to 48
> cfg.method            = 'montecarlo';
> cfg.statistic            = 'ft_statfun_depsamplesT';
> cfg.correctm          = 'cluster';
> cfg.clusteralpha     = 0.05;
> cfg.clusterstatistic  = 'maxsum';
> cfg.minnbchan       = 2;
> cfg.tail                    = 0;
> cfg.clustertail         = 0;
> cfg.alpha                = 0.05;
> cfg.numrandomization = 500;
>
> % 3. Find the channel neighbours for spatial clustering
>
> cfg_neighb.method    = 'distance';
> cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, Tfr_Ogt_ogt{1,1});
>
> ft_neighbourplot(cfg_neighb, Tfr_Ogt_ogt{1:1})% to check neighbours
>
> %------------------------
>
> % 4. Setting the design for the cluster permutation test
>
> Nsubj  = 33;
> design = zeros(2, Nsubj*2);
> design(1,:) = [1:Nsubj 1:Nsubj];
> design(2,:) = [ones(1,Nsubj) ones(1,Nsubj)*2];
>
> cfg.design = design;
> cfg.uvar   = 1;
> cfg.ivar   = 2;
>
> [stat] = ft_freqstatistics(cfg, Tfr_Ogt_ogt{:}, Tfr_Ogt_low{:});
>
> % ------------------------------------------------------------------------
>
> Until here I get no error messages and the 'stat' variable seems to have
> been created (I got 14 negative clusters). Though *when I try plotting
> it, I get the following error message*;
>
> Input:
> % 5. Plot with ft_clusterplot:
>
> cfg = [];
> cfg.alpha  = 0.05;
> cfg.parameter = 'stat';
> cfg.zlim   = 'maxmin';
> cfg.layout = 'acticap-64ch-standard2.mat';
> ft_clusterplot(cfg, stat);
>
> Output:
>
> >> cfg = [];
> cfg.alpha  = 0.05;
> cfg.parameter = 'stat';
> cfg.zlim   = 'maxmin';
> cfg.layout = 'acticap-64ch-standard2.mat';
> ft_clusterplot(cfg, stat);
> the input is freq data with 64 channels, 48 frequencybins and 37 timebins
> reading layout from file acticap-64ch-standard2.mat
> the call to "ft_prepare_layout" took 0 seconds and required the additional
> allocation of an estimated 0 MB
>
> *Error using ft_clusterplot (line 153)if you input time-frequency data
> this only works if either frequency or time is a singleton dimension*
>
> Does anyone know what I can do to plot my data correctly? I would really
> appreciate any inputs.
>
> Best,
>
> --
> *Bruno*
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>


-- 
*Mustafa Yavuz *

M.Sc. in Neuroscience
RA in HUBAL Neuroimaging Unit
Department of Neuroscience
İstanbul University
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