[FieldTrip] Error using ft_clusterplot (line 153)
Bruno Mansur
brunommansur at gmail.com
Wed Jun 2 22:13:47 CEST 2021
Dear Mustafa,
Yes, I fear you're right. I'll try to perform something similar using
'ft_multiplotTFR' or 'ft_topoplotTFR'.
Thank you for your hints and time!
Best,
Am Mi., 2. Juni 2021 um 17:12 Uhr schrieb MUSTAFA YAVUZ via fieldtrip <
fieldtrip at science.ru.nl>:
> Dear Bruno,
>
> Thank you for your clarification. I guess the difference between your
> example and the FT documentation is that the example on the webpage only
> focuses on 1 frequency bin (e.g. 20 Hz). I guess the difference with your
> example would be this which affects your data structure to be plotted.
>
>
> Best wishes,
> Mustafa
>
> Bruno Mansur via fieldtrip <fieldtrip at science.ru.nl>, 2 Haz 2021 Çar,
> 17:30 tarihinde şunu yazdı:
>
>> 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
>> _______________________________________________
>> 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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