[FieldTrip] ft_singleplotTFR issues.

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Tue Mar 5 11:11:17 CET 2019 

In this case, I don’t believe in coincidence. I suspect that the time axis in your ‘erp’ variable does not align well with the cfg.toi you try to extract with ft_freqanalysis,  in combination with the time-frequency window specified, which is longer (0.5 s) in the ‘low’ frequency case than in the ‘high’ frequency case.

Jan-Mathijs


On 5 Mar 2019, at 11:06, Marion Vincent <marion.vincent at univ-lille.fr<mailto:marion.vincent at univ-lille.fr>> wrote:

Hi Jan-Mathijs,

Thanks for your reply. I noticed there is no time matrix in the tfreq_Low  structure (from ft_freqanalysis(cfg, erp)).
But I can’t figure out why.
I’ve compared my erp matrix and my code for setting the ft_freqanalysis  parameters with ones from examples and it seems that my structures are welle shaped.

Do you have any idea ?
Moreover I can’t figure out how my hig frequency analysis works fine compraed to the low frequency one. Maybe it worked by chance.

Thanks,
Marion


Marion VINCENT
Eng., PhD , CNRS Research Engineer
Tel: +33 607 59 46 76

Laboratoire SCALab UMR CNRS 9193
Université Lille 3
BP 60149
59653 Villeneuve d'Ascq CedexI
http://scalab.cnrs.fr<http://scalab.cnrs.fr/>
--------------------------------------------
L’Imaginarium / SCV-IrDIVE Equipex
99a Boulevard Descat
59200 Tourcoing
http://www.irdive.fr<http://www.irdive.fr/>/<http://www.irdive.fr/>

De : Schoffelen, J.M. (Jan Mathijs)<mailto:jan.schoffelen at donders.ru.nl>
Envoyé le :lundi 4 mars 2019 18:11
À : FieldTrip discussion list<mailto:fieldtrip at science.ru.nl>
Objet :Re: [FieldTrip] ft_singleplotTFR issues.

Hi Marion,

The assertion on line 177 (in the current version of the code this is line 178) of ft_singleplotTFR checks for the presence of a ‘freq’ and ‘time’ field in your data. It seems as if your data doesn’t meet this expectation. Hence the error.

Jan-Mathijs

J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands

On 4 Mar 2019, at 16:02, Marion Vincent <marion.vincent at univ-lille.fr<mailto:marion.vincent at univ-lille.fr>> wrote:

Dear all,

I’m having some troubles using the ft_singleplotTFR for time-frequency analysis.
I’ve tried 2 different TF analysis : 'mtmfft' for low frequencies and ‘'mtmconvol'’ for high frequencies.

However I’ve got the Following error for the single plot of the low freq TF (but it works for high freq TF).

****************************
Error using ft_singleplotTFR (line 177)
please use ft_singleplotER for time-only or frequency-only data
****************************

Does anyone have any idea ? I’ve put the entire code below.

Thanks !
Marion



%% TIME-FREQUENCY ANALYSIS
close all
clear all

%% ************************ INITIALIZATION ******************
%% Parameters to change
EXP             =   '1';
seg_window      =   [1 1.1]; % in seconds %preStim/postStim
cond            = 1; % number of the experimental condition 1 to 4
Baseline_Window      = [-1 0] ; %as the baseline lasts 1s before the stimulus onset

%%  initialize fieldtrip
startup()

%% initialize paths
path_Biosemi  = 'C:\Users\Marion\Documents\EEG\Prosodie - Angele\AV-Exps';
path_data='C:\Users\Marion\Documents\MATLAB\EEG_AV-Exps';

%% subjects list
load(fullfile(path_data, 'data', 'Participants_List.mat'));

for i=1:27
    subjects{i,1}=list_Participants(i);
end
clear list_Participants i

%% ************************ TIME-FREQUENCY DOMAIN ANALYSIS --- WANG et al. 2017 %%%%%%%%
% LOW FREQUENCIES: 2-30 Hz => Hanning multitaper %% fixed window length
% HIGH FREQUENCIES: 25-100 Hz => Slepian multitaper

tic
nsubj = 4;%numel(subjects);

tfreq_Low  = cell(1,nsubj);
tfreq_High  = cell(1,nsubj);

for i=1:nsubj
    % load the erp data
    datapath = strcat(path_data, '/data')
    results_path=fullfile(datapath,['Participant_' num2str(subjects{i})]);

    datafile = fullfile(results_path, ['erp_Cond' num2str(cond) '.mat']);
    % load the ERP data of subject i from disk
    load(datafile);

    erp=eval(['ERP_cond' num2str(cond)]);

    % Low-frequencies 2-30 Hz
    cfg              = [];
    cfg.output       = 'pow';
    cfg.method       = 'mtmfft';
    cfg.taper        = 'hanning';
    cfg.foi          = 2:2:30;                         % analysis 2 to 30 Hz in steps of 2 Hz
    cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
    cfg.toi          = -1:0.05:1.1;                    % time window "slides" from -1 to 1.1 sec in steps of 0.05 sec (50 ms)
    tfreq_Low = ft_freqanalysis(cfg, erp);

%     % Visualization single plot
%     cfg = [];
%     cfg.channel      = {'A1'};
%     figure
%     ft_singleplotTFR(cfg, tfreq_Low);


    % High frequencies 25-100 Hz
    cfg              = [];
    cfg.output       = 'pow';
    cfg.method       = 'mtmconvol';
    cfg.taper        = 'dpss';
    cfg.foi          = 25:5:100;                         % analysis 25 to 100 Hz in steps of 5 Hz
    h  =  ones(length(cfg.foi),1).*20 % vector 1 x numfoi, the amount of spectral smoothing through multi-tapering.
    % Note that 4 Hz smoothing means plus-minus 4 Hz, i.e. a 8 Hz smoothing box.
    cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.2;   % length of time window = 0.2 sec FIXED
    cfg.toi          = -1:0.05:1.1;                  % time window "slides" from -0.1 to 1 sec in steps of 0.01 sec (10 ms)
    tfreq_High = ft_freqanalysis(cfg, erp);

    % Visualization single plot
    cfg = [];
    cfg.channel      = {'A1'};
    figure
    ft_singleplotTFR(cfg, tfreq_High);


    % Visualization single plot
    cfg = [];
    cfg.layout = 'C:\Users\Marion\Documents\MATLAB\EEG_AV-Exps\biosemi128.lay';
    ft_multiplotTFR(cfg, TFRhann_HF);

end


Marion VINCENT
Eng., PhD , CNRS Research Engineer
Tel: +33 607 59 46 76

Laboratoire SCALab UMR CNRS 9193
Université Lille 3
BP 60149
59653 Villeneuve d'Ascq Cedex
http://scalab.cnrs.fr<http://scalab.cnrs.fr/>
--------------------------------------------
L’Imaginarium / SCV-IrDIVE Equipex
99a Boulevard Descat
59200 Tourcoing
http://www.irdive.fr<http://www.irdive.fr/>/<http://www.irdive.fr/>

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