[FieldTrip] Baseline removal errors in trials preprocessing
Stephen Whitmarsh
stephen.whitmarsh at gmail.com
Thu Jan 17 18:50:16 CET 2019
Hi Marion,
I would check your time axis.
I never use ft_definetrial like that (I make my own .trl field), so I'm not
sure it went through correctly with the offset (t=0).
So check your data_Raw.time{1}. Does it really go from -0.1 to 1.0? If not,
Julian's point is right, and your point on that is 'first point' might be
explained as well, if I understood that correctly.
Cheers,
Stephen
On Thu, 17 Jan 2019 at 18:29, Marion Vincent <marion.vincent at univ-lille.fr>
wrote:
> Dear Stephen,
> Thanks for your comments.
> In fact I only used the cgf1, cfg2.. for plotting the figure I sent you.
> So it was not my «real» code.
> But you’re rigth cleaning the cfg will prevent some errors.
> I’ve done so and still have some errors: (for each case, I compared it to
> a personnal calculation)
> If I use the ‘all’ default cfg.baselinewindow => I have the result I
> expected: the Baseline is the mean value of all the signal. (cf. figure
> Baseline_AllSignal)If I use a given time window (here from 0.1 to 0 sec
> before the stimulsu onset) => in fieldtrip, the Baseline is only the «first
> point» of the raw signal, but not its mean value on the Baseline window (as
> in my own calculation: cf. figure Baseline_TimeWindow). I also tried with
> exorbitant window [-10000 0], [0 0.1], etc ) and each time I Always have
> the exact same result for the filedtrip calculation.
> Here is my entire code(I hope it will be clearer):
> **************************************************************
> seg_window=[0.1 1]; % in seconds %preStim/postStim
> trig_Type=[1 5 2 6 3 7 4 8]; % trigger value
> load(filename_Trig);
> % ** READ FILE INFO
> % read the header information and the events from the data
> hdr = ft_read_header(filename_Data);
> % Config
> cfg= [];
> cfg.dataset = filename_Data;
> % **RE-REFERENCES
> cfg.reref = 'yes';
> cfg.refchannel = {'EXG3', 'EXG4'} ; % electrode 131/132 // cell-array
> with new EEG reference channel(s), this can be 'all' for a common average
> reference
> cfg.refmethod = 'avg'; % 'avg', 'median', or 'bipolar' for bipolar
> derivation of sequential channels (default = 'avg')
> % ** TRIAL DEFINITION
> event_All = ft_read_event(filename_Data);
> % Select only the trigger codes, not the battery and CMS status
> sel = find(strcmp({event_All.type}, 'STATUS'));
> event_All = event_All(sel);
> cfg.eventType=[trig_Type(1) trig_Type(2)];
> cfg.trialfun = 'AVExp_trialfun';
> cfg.trialdef.pre = seg_window(1);
> cfg.trialdef.post = seg_window(2);
> cfg.Fs=hdr.Fs; % convert seconds in sample
> cfg = ft_definetrial(cfg);
> % Remove trials from Cartool selection
> cfg.trl(find(Triggers{num_Cond}(:,1)==0),:) = [];
> data_Raw = ft_preprocessing(cfg);
> % Plot data to check
> figure ; chan_num=1;
> trial_num=1;
> figure;
> plot(data_Raw.trial{trial_num}(chan_num,:));
> % ** BASELINE CORRECTION: BASELINE IS ALL THE SIGNAL
> %baseline correct the raw data structure, automatic
> cfg = [] ;
> cfg.demean = 'yes';
> cfg.baselinewindow = 'all';
> data_Raw_reref = ft_preprocessing(cfg, data_Raw);
> % Manual correction test
> for trial_num=1:length(data_Raw.trial)
> for chan_num=1:length(data_Raw.label)
> Signal=data_Raw.trial{trial_num}(chan_num,:);
> baseline_value=mean(Signal); % for comparison with the default
> value of
>
> data_Raw_reref_Manual.trial{trial_num}(chan_num,:)=data_Raw.trial{trial_num}(chan_num,:)-baseline_value*ones(1,length(Signal));
> end
> end
> % plot comparison
> figure;chan_num=1;
> trial_num=1;
> hold all
> plot(data_Raw_reref.trial{trial_num}(chan_num,:));
> plot(data_Raw_reref_Manual.trial{trial_num}(chan_num,:));
> legend('FieldTrip','Manual');
> title('Baseline is all the signal');
> % ** BASELINE CORRECTION: BASELINE IS THE MEAN VALUE OF A WINDOW of 0.1sec
> before the stimulus onset
> %baseline correct the raw data structure, automatic
> cfg = [] ;
> cfg.demean = 'yes';
> cfg.baselinewindow = [-0.1 0] ; %as the baseline lasts 0.1 s before
> the stimulus onset
> data_Raw_reref_1 = ft_preprocessing(cfg, data_Raw);
> % Manual correction test for trial 1 - comparison to automatic calculation
> for trial_num=1:length(data_Raw.trial)
> for chan_num=1:length(data_Raw.label)
> Signal=data_Raw.trial{trial_num}(chan_num,:);
> baseline_window=[1 round(hdr.Fs*0.1)];% because baseline lasts
> 0.1 s before the stimulus onset
> baseline_value=mean(Signal(baseline_window(1):baseline_window(2)));
>
> data_Raw_reref_Manual_1.trial{trial_num}(chan_num,:)=data_Raw.trial{trial_num}(chan_num,:)-baseline_value*ones(1,length(Signal));
> end
> end
> % plot comparison
> figure;chan_num=1;
> trial_num=1;
> hold all
> plot(data_Raw_reref_1.trial{trial_num}(chan_num,:));
> plot(data_Raw_reref_Manual_1.trial{trial_num}(chan_num,:));
> legend('FieldTrip','Manual');
> title('Baseline is a given time window’);
> **************************************************************
> I’m sure it’s a silly mistake, but I really can’t find it.
> 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 Cedex
> http://scalab.cnrs.fr
> --------------------------------------------
> L’Imaginarium / SCV-IrDIVE Equipex
> 99a Boulevard Descat
> 59200 Tourcoing
> http://www.irdive.fr/
> De: Stephen Whitmarsh
> Envoyé le:jeudi 17 janvier 2019 15:03
> À: 'FieldTrip discussion list'
> Objet:Re: [FieldTrip] Baseline removal errors in trials preprocessing
>
>
> Dear Marion,
>
>
>
> Your script is a bit messy. I would start with:
>
> 1) Always clear your cfg before calling a FT function. Don’t go
> around saving different cfg’s. This is the nr. 1 cause of confusing results
> J
>
> 2) Load/segment etc. your data first with ft_preprocessing. Then call
> ft_preprocessing again to baseline correct, entering the output of the
> first run.
>
> I have a hunch that might fix your problem. So, something like:
>
>
>
> % load your data, apply rereferencing and segment in one go
>
> cfg = [];
>
> cfg.dataset = filename_Data;
>
> cfg.reref = 'yes';
>
> cfg.refchannel = {'EXG3', 'EXG4'} ;
>
> cfg.refmethod = 'avg';
>
> cfg.trl = … ;
>
> cfg = ft_definetrial(cfg);
>
> data_Raw = ft_preprocessing(cfg);
>
>
>
> % somehow plot your data to check
>
> figure ; plot(data_Raw.trial{1}(1, :)) ;
>
>
>
> % baseline correct your raw data structure, method 1
>
> cfg = [] ;
>
> cfg.demean = ‘yes’ ;
>
> cfg.baselinewindow = [0 0.1] ;
>
> data_Raw_reref_1 = ft_preprocessing(cfg, data_Raw);
>
>
>
> % somehow plot your data to check
>
> figure ; plot(data_Raw_reref_1.trial{1}(1, :)) ;
>
>
>
> % baseline correct your raw data structure, method 2
>
> cfg = [] ;
>
> cfg.demean = ‘yes’ ;
>
> cfg.baselinewindow = [-1 -0.1] ; % or whatever
>
> data_Raw_reref_2 = ft_preprocessing(cfg, data_Raw);
>
>
>
> % somehow plot your data to check
>
> figure ; plot(data_Raw_reref_2.trial{1}(1, :)) ;
>
>
>
> And oh, wait, I see what you did there… Don’t use different variables for
> your cfg, (e.g. cfg1, cfg2, etc.). See the mistake? Those are too easy to
> make if you don’t do something like the above.
>
>
>
> Cheers and good FieldTripping!
>
> Stepen
>
>
>
>
>
>
>
> From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Marion
> Vincent
> Sent: Thursday, January 17, 2019 2:00 PM
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Baseline removal errors in trials preprocessing
>
>
>
> Dear Stephen,
>
>
>
> Here is my script :
>
>
>
> %segmentation
>
> seg_window=[0.1 1]; % in seconds %preStim/postStim
>
>
>
> %config
>
> cfg= [];
>
> cfg.dataset = filename_Data;
>
>
>
> %% *********** TRIAL DEFINITION PART *********** (that works )
>
> […]
>
> cfg = ft_definetrial(cfg);
>
>
>
> % *********** Re-References *********** (that also works )
>
> cfg.reref = 'yes';
>
> cfg.refchannel = {'EXG3', 'EXG4'};% electrode 131/132 // cell-array with
> new EEG reference channel(s), this can be 'all' for a common average
> reference
>
> cfg.refmethod = 'avg'; % 'avg', 'median', or 'bipolar' for bipolar
> derivation of sequential channels (default = 'avg')
>
>
>
> data_Raw = ft_preprocessing(cfg);
>
>
>
> %% *********** Baseline ***********
>
> cfg.demean = 'yes';
>
>
>
> cfg1=cfg;
>
> cfg1.baselinewindow = [-seg_window(1) 0 ];
>
> cfg2=cfg;
>
> cfg2.baselinewindow = [0 0.1];
>
> cfg3=cfg;
>
> cfg3.baselinewindow = 'all';
>
>
>
> data1 = ft_preprocessing(cfg1);
>
> data2 = ft_preprocessing(cfg2);
>
> data3 = ft_preprocessing(cfg3);
>
>
>
>
>
> ð I’ve attached the figure with the results.
>
>
>
> PS : In fact I made a mistake in my previous email : the result wasn’t the
> same when the Baseline window was ‘all’.
>
>
>
> Let me know if you need more informations.
>
> Thanks for your help.
>
>
>
> 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 Cedex
> http://scalab.cnrs.fr
> --------------------------------------------
> L’Imaginarium / SCV-IrDIVE Equipex
> 99a Boulevard Descat
> 59200 Tourcoing
> http://www.irdive.fr <http://www.irdive.fr/> /
>
>
>
> De : Stephen Whitmarsh <mailto:stephen.whitmarsh at gmail.com>
> Envoyé le :jeudi 17 janvier 2019 11:51
> À : 'FieldTrip discussion list' <mailto:fieldtrip at science.ru.nl>
> Objet :Re: [FieldTrip] Baseline removal errors in trials preprocessing
>
>
>
>
>
> Dear Marion,
>
>
>
> It sounds it might indeed be something as simple as a typo. Could you
> paste the part of your script – from baseline removal to plotting (where
> you don’t see a difference) - so we can take a look?
>
>
>
> Cheers,
>
> Stephen
>
>
>
> From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:
> fieldtrip-bounces at science.ru.nl> > On Behalf Of Marion Vincent
> Sent: Thursday, January 17, 2019 10:37 AM
> To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Baseline removal errors in trials preprocessing
>
>
>
> Dear FIeldtrip users,
>
>
>
> I’m new in using Fieldtrip for EEG processing and I’ve encountred some
> issues while removing the Baseline of my trials.
>
>
>
> I’m working on EEG signals recorded with the BioSemi system. My
> pre-processing method is :
>
> (1) Re-referecing the channels (necessary with BioSemi)
>
> (2) Trial definition
>
> (3) Baseline removal
>
>
>
> I’ve read on the documentation that ft_preprocessing xcan have several cfg
> parameter for the Baseline removal :
>
>
>
> % cfg.demean = 'yes';%'no' or 'yes', whether to apply baseline correction
> (default = 'no')
>
> % cfg.baselinewindow = 'all';%[begin end] ;%in seconds, the default is the
> complete trial (default = 'all')
>
> % cfg.detrend = 'no'; %'no' or 'yes', remove linear trend from the
> data (done per trial) (default = 'no')
>
>
>
> I wanted to remove a Baseline defined as the average of a given window
> preceeding my stimulus onset.
>
>
>
> I tried to use : cfg.baselinewindow = [-0.5 0 ]; cfg.baselinewindow = [0
> 0.1] or the default window .
>
> But the problem is that I always have the same result, no matter the
> window I use : the first point of my trial is put to zero and substracted
> to all my trial.
>
>
>
> I’m sure I’m doing something wrong (and that the answer is very simple),
> but I can’t manage to understand what is the issue.
>
>
>
> Do you have any advice ?
>
>
>
> Thanks !
>
> Marion
>
>
>
> Marion VINCENT
> Eng., PhD , CNRS Research Engineer
>
>
>
>
>
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