[FieldTrip] High pass filtering before epoching

[Julian Keil]

Hello Frans,

I don’t know whether there is a specific reason that TF segments first and filters later, but here’s what I do in order to be sure that the filtering is done on the whole epoch (https://urldefense.com/v3/__https://github.com/BioPsychKiel/SpringSchool2022/blob/main/track_02/01_Code/sc01_preproc.m__;!!HJOPV4FYYWzcc1jazlU!_yF8KxqbQ9i7O04I1jY6rUBExCiDZCkq2juuIOst9PZY0BoNkNcN_XM_EdKi85VuqUKBBTFIkjVBq0cmPuLpKQN0Bg$ ):

% 1.1. First, read in the header to define the trials
cfg = []; % Always clear the configuration
cfg.dataset = [inpath,indat(v).name]; % Set the dataset
cfg.trialdef.eventtype = 'Markers'; % We now know that the trigger channel is called 'Stimulus'
cfg.trialdef.eventvalue = {20,30}; % Define the relevant triggers
cfg.trialdef.prestim = 1.5; % Seconds before the stimulus
cfg.trialdef.poststim = 1.5; % Seconds after the stimulus
cfg = ft_definetrial(cfg); % Store the trial definition
% 1.2. Save the trial-definition
trl = cfg.trl;
% 1.3. Then define the entire dataset
cfg = []; % Always clear the configuration
cfg.dataset = [inpath,indat(v).name]; % Set the dataset
cfg.trialdef.ntrials = 1; % One long trial to cover the entire dataset
cfg = ft_definetrial(cfg); % Store the trial definition
%% 2. Preprocessing
% This step will read, filter and cut the raw data
% 2.1. Read in the raw data and filter
cfg.demean = 'yes'; % Remove mean across time to get rid of offset
cfg.hpfilter = 'yes'; % Highpassfilter to remove slow drifts
cfg.hpfreq = .1; % Highpass frequency. 0.1 removes most slow drifts
cfg.hpfilttype = 'firws'; % Type of filter
cfg.lpfilter = 'yes'; % The same for lowpass
cfg.lpfreq = 45; % 50Hz line noise destroys the data, only take data below
cfg.lpfilttype = 'firws'; % Again the type
data_p = ft_preprocessing(cfg);

% 2.2. Cut the data according to the trial definition
cfg = [];
cfg.trl = trl; % Use the trl-structure defined above

data_t = ft_redefinetrial(cfg,data_p);

Please not that this takes quite a bit longer than doing it the FT-way.
I hope this helps,

Julian


> Am 15.02.2023 um 11:33 schrieb Frans Nord via fieldtrip <fieldtrip at science.ru.nl>:
> 
> Hello mailing-list,
> 
> I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:
> 
> "We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."
> 
> Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:
> 
> cfg = [];
> cfg.continuous           ='yes';
> cfg.trialfun                = 'ft_trialfun_general';
> cfg.trialdef.eventtype       = 'STATUS';
> cfg.trialdef.eventvalue      = {1,2,3,4}; % Trigger values
> cfg.trialdef.prestim         =.5; % -500 ms before the stimulation
> cfg.trialdef.poststim        = 2; % +2000ms after the stimulation
> cfg.dataset            = path_to_dataset;             % set the name of the dataset
> cfg            = ft_definetrial(cfg);   % read the list of the specific stimuluscfg.hpfilter       = 'yes';
> cfg.hpfreq         = 1;[data]                     =ft_preprocessing(cfg);
> 
> I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.
> 
> Thank you for providing the Fieldtrip toolbox
> Best
> Frans
> 
> [1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!_yF8KxqbQ9i7O04I1jY6rUBExCiDZCkq2juuIOst9PZY0BoNkNcN_XM_EdKi85VuqUKBBTFIkjVBq0cmPuKb0Uu2dw$  <https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!4hjKg111dQ7s9-L3G_ddKy01SDzvgiEvo8gLx_R-WDx6Qxj6JJS0HuEwuUx1atexqoHmVc8kvd5ouM4p4smQ$>_______________________________________________
> fieldtrip mailing list
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> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!_yF8KxqbQ9i7O04I1jY6rUBExCiDZCkq2juuIOst9PZY0BoNkNcN_XM_EdKi85VuqUKBBTFIkjVBq0cmPuL82C-wOg$ 

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