[FieldTrip] problems using fieldtrip for source reconstruction EEG

Mon Jan 7 11:30:16 CET 2019

Hello Alex,

I have tried the tutorial you mention, but as I stated above, I get error
related with the definition of the structure (This function requires
'timelock' or 'freq' data as input, see ft_datatype_timelock or
ft_datatype_freq.). We dont really know how to obtain this from data. Do we
have to add something more to obtain timelock and freq?
Example:

EEG=load(filename);
data=EEG.data;
cfg = [];
cfg.xlim = [-0.2 1.0];
cfg.ylim = [-1e-13 3e-13];
cfg.channel = 'A1';
figure; ft_singleplotER(cfg,data);

Thank you in advance,
Irene

El lun., 7 ene. 2019 a las 11:20, Alexis Pérez (<
alexisperezbellido at gmail.com>) escribió:

> Hi Irene,
>
> here you have different examples on how you can plot data in fieldtrip.
> http://www.fieldtriptoolbox.org/tutorial/plotting/
>
> I recommend you to follow the tutorial by running the little snippets of
> code and trying to understand:
> 1 what are the fields that your data structure should contain in order to
> be plotted (e.g. if you want to plot timefrequency amplitide
> representations you must have a power representation).
> 2 how each of the cfg. arguments modify your plot (you can also use the
> matlab help command in each plotting function to see a description of the
> different plot features that you can modify).
> 3 what different types of data you can find and what are the different
> ways to plot them.
>
> Once you have understood how yo plot the data in the fieldtrip examples,
> then you can start to generalize and customize those functions to your own
> needs.
>
> In your particular example, if you want to plot the topology then you must
> use ft_topoplotER (and not ft_singleplotER). Remember to indicate what is
> your helmet sensor/electrodes layout otherwise you will get errors or
> incorrect representation of your data.
>
> Good luck and patience.
>
> alex
>
> On Mon, Jan 7, 2019 at 10:36 AM Irene Varela Leniz <
> irene.varela at alumni.mondragon.edu> wrote:
>
>> 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>)
>> 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
>>> ).
>>>
>>> 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/
>>>
>>> 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 09:57 schrieb Irene Varela Leniz <
>>> 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>)
>>> 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>:
>>>>
>>>> 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
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>>
>>>>
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>>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>>
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>>
>
>
> --
> Alexis Pérez-Bellido, PhD
> Donders Institute for Brain, Cognition and Behavior, Nijmegen, Netherlands
> Prediction & Attention group
> web: https://www.predictivebrainlab.com/ <http://www.predatt.com/>
> gmail: alexisperezbellido at gmail.com
> skype: alexisperezbellido
>
>
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