[FieldTrip] problems using fieldtrip for source reconstruction EEG
Julian Keil
julian.keil at gmail.com
Mon Jan 7 11:15:02 CET 2019
Hi Irene,
ft_topoplotER requires indeed timelock data, i.e. data in which you have computed the average over trials. Given that you wrote before that you are using resting-state data, I’m not sure this is the right function you need.
Can you post the content of the struct you want to plot?
In any way, if you are hitting a wall in using fieldtrip, I suggest starting with one of the many tutorials to get a sense of how things work. Just diving in with your own data without knowing exactly what each function does will be rather frustrating.
Best,
Julian
________________
Prof. Dr. Julian Keil
Biological Psychology
Olshausenstrasse 62 - R. 306
24118 Kiel, Germany
+49 - 0431 - 880 - 4872
http://www.biopsych.uni-kiel.de/en
> Am 07.01.2019 um 10:34 schrieb Irene Varela Leniz <irene.varela at alumni.mondragon.edu>:
>
> Hi Julian,
>
> I have read about them in Fieldtrip documentation but I still dont manage to do nothing. I am looking for a topographic visualization of data and I am interesed in using Fieldtrip. Moreover, whenever I try different command I get the following error:
>
> Error using ft_checkdata (line 525)
> This function requires 'timelock' or 'freq' data as input, see ft_datatype_timelock or ft_datatype_freq.
> Error in ft_singleplotER (line 133)
> varargin{i} = ft_checkdata(varargin{i}, 'datatype', {'timelock', 'freq'});
>
> The data comes from eeglab using eeglab2fieldtrip function, so that we have the data stored in a struct.
>
> Thank you in advance,
> Irene
>
> El lun., 7 ene. 2019 a las 10:27, Julian Keil (<julian.keil at gmail.com <mailto:julian.keil at gmail.com>>) escribió:
> Hi Irene,
>
> it helps if you describe exactly what you want to do (I don’t mean to be rude or patronizing, but check here for suggestions: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202>).
>
> There are many ways to visualize resting state EEG signals, and you don’t need fieldtrip for all of them.
> E.g., if you just want to plot the timecourse of the data, you can use the matlab built-in „plot“ function (e.g. use something like "plot(data.time{1},data.trial{1})“ to plot one trial). If you want to explore your data, ft_databrowser is your friend http://www.fieldtriptoolbox.org/faq/how_can_i_use_the_databrowser/ <http://www.fieldtriptoolbox.org/faq/how_can_i_use_the_databrowser/>
>
> Best,
>
> Julian
>
> ________________
> Prof. Dr. Julian Keil
>
> Biological Psychology
> Olshausenstrasse 62 - R. 306
> 24118 Kiel, Germany
>
> +49 - 0431 - 880 - 4872
> http://www.biopsych.uni-kiel.de/en <http://www.biopsych.uni-kiel.de/en>
>
>
>> Am 07.01.2019 um 09:57 schrieb Irene Varela Leniz <irene.varela at alumni.mondragon.edu <mailto:irene.varela at alumni.mondragon.edu>>:
>>
>> Good morning Julian,
>>
>> Can you help me with plotting some resting state EEG signals? I am new in Fieldtrip and I dont find clear information about this topic and I dont really know how to do plottings in Fieldtrip. I feel like the fieldtrip documentation is a little bit weak....
>>
>> Thank you in advance,
>> Best regards,
>>
>> Irene Varela
>>
>> El vie., 4 ene. 2019 a las 14:08, Julian Keil (<julian.keil at gmail.com <mailto:julian.keil at gmail.com>>) escribió:
>> Hi Irene,
>>
>> what is the reason to use the extra checkdata step?
>> The function checks if the input data has the correct „datatype“ field.
>> Since you probably don’t have that field, the function will throw an error.
>>
>> Also, I’d recommend using the eeglab2fieldtrip-function to get from EEGlab .set to a fieldtrip-like structure.
>>
>> Best,
>>
>> Julian
>>
>>
>>> Am 04.01.2019 um 12:47 schrieb Irene Varela Leniz <irene.varela at alumni.mondragon.edu <mailto:irene.varela at alumni.mondragon.edu>>:
>>>
>>> Hi,
>>>
>>> I am a researcher in Mondragon University working on source reconstruction of EEG data. I am new at fieldtrip and I feel a little bit lost about this software. I have some errors in a code I have developed but I do not manage to solve them. Could you please help me?
>>>
>>> I want to plot EEG data of a channel called 'A1' which is the first row in a 2D matrix variable called data, which is inside EEG structure. The code I have developed is below and I get the following error:
>>>
>>> Error using ft_checkdata (line 525)
>>> This function requires 'timelock' or 'freq' data as input, see ft_datatype_timelock or ft_datatype_freq.
>>>
>>> The code is the following:
>>> clc; clear all; close all;
>>> clear variables
>>> restoredefaultpath; % set a clean path
>>> main='E:\';
>>> cd='E:\fieldtrip-20181217'; % change this
>>> addpath(cd);
>>>
>>> ft_defaults;
>>> filename = "E:\PBLdata\O200_RS1_final.set"; %cambiar aqui y poner vuestro directorio
>>> load(filename, '-mat'); %Create EEG struct
>>> location = EEG.chanlocs;
>>> data = EEG.data;
>>>
>>> cfg = [];
>>> cfg.xlim = [-0.2 1.0];
>>> cfg.ylim = [-1e-13 3e-13];
>>> cfg.channel = 'A1';
>>> datos = data(1,:);
>>> Ndata = numel(datos);
>>> for i=1:Ndata
>>> % check if the input data is valid for this function
>>> datos(i) = ft_checkdata(datos(i), 'datatype', {'timelock', 'freq'});
>>> end
>>>
>>> figure; ft_singleplotER(cfg,datos);
>>>
>>> Thank you in advance,
>>>
>>> Irene
>>>
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>>> fieldtrip mailing list
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>>> https://doi.org/10.1371/journal.pcbi.1002202 <https://doi.org/10.1371/journal.pcbi.1002202>
>>
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