[FieldTrip] Baseline removal errors in trials preprocessing

Thu Jan 17 15:16:58 CET 2019

Dear Julian, 

seg_window=[0.1 1]; % in seconds %preStim/postStim

Does that mean, you segment your data to 0.1 s to 1 s after the stimulus?
In that case, there is no data to use prior to 0.1 later on.

The seg_window I used was to defined the trials (prestim to poststim interval).
Then in my one trial definition function  I define my trial as the interval [t0-preStim ; t0+postStim], with t0 the stimulus onset.
⇨ My trial goes from 0.1s before t0 to 1 s after.
That is why the preStim value is positive in seg_window.

So, these two statements:
cfg1=cfg;
cfg1.baselinewindow = [-seg_window(1) 0 ];
cfg2=cfg;
cfg2.baselinewindow = [0 0.1];
are basically identical, as the interval -0.1 to 0 (cfg1) and 0 to 0.1 (cfg2) will both contain no data.
Please double check this with the seg_window set to [-0.1 1]

I think I might not understood how to pass the time interval in the cfg.baselinewindow.
For me as I stated [ - seg_window(1)  ;  0], in had in mind to take the interval [ - 0.1 ; 0] before the stimulus onset (at t0=0) . 

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 : Julian Keil
Envoyé le :jeudi 17 janvier 2019 14:57
À : FieldTrip discussion list
Objet :Re: [FieldTrip] Baseline removal errors in trials preprocessing

Dear Marion,

when you state: 
seg_window=[0.1 1]; % in seconds %preStim/postStim

Does that mean, you segment your data to 0.1 s to 1 s after the stimulus?
In that case, there is no data to use prior to 0.1 later on.

So, these two statements:

cfg1=cfg;
cfg1.baselinewindow = [-seg_window(1) 0 ];
cfg2=cfg;
cfg2.baselinewindow = [0 0.1];

are basically identical, as the interval -0.1 to 0 (cfg1) and 0 to 0.1 (cfg2) will both contain no data.

Please double check this with the seg_window set to [-0.1 1]

Hope that helps,

Julian

On Thu, Jan 17, 2019 at 2:29 PM Marion Vincent <marion.vincent at univ-lille.fr> wrote:
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);
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/
De: Stephen Whitmarsh
Envoyé le:jeudi 17 janvier 2019 11:51
À: 'FieldTrip discussion list'
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> On Behalf Of Marion Vincent
Sent: Thursday, January 17, 2019 10:37 AM
To: 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

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190117/f2fb644e/attachment-0002.html>