[FieldTrip] Error using ft_clusterplot (line 153)

[Bruno Mansur]

Dear Mustafa,

Thanks a lot for your answer!

The result I'm pursuing is similar to the one in the tutorial found in the
fieldtrip webpage in the section '*within subjects experiments*':
https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq/#within-subjects-experiments

There they use the function *ft_clusterplot* to plot the data structure in
a figure containing subplots, spaced by a certain time interval. I would
like to reproduce that with my data.
Besides that, I don't know if the *ft_multiplotTFR* function would account
for the spatial resolution of the cluster formations, because it just plots
the freq range over a time axis for each electrode, independently.

Best,

Am Di., 1. Juni 2021 um 17:48 Uhr schrieb MUSTAFA YAVUZ via fieldtrip <
fieldtrip at science.ru.nl>:

> 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
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>


-- 
*Bruno de Matos Mansur, M.Sc.*
Neurocybernetics und Rehabilitation
University Hospital Magdeburg
Leipziger Strasse 44, 39120 Magdeburg, Germany
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