<div dir="ltr"><div>Dear Marion,</div><div><br></div><div>when you state: <br></div><div>seg_window=[0.1 1]; % in seconds %preStim/postStim</div><div><br></div><div>Does that mean, you segment your data to 0.1 s to 1 s after the stimulus?</div><div>In that case, there is no data to use prior to 0.1 later on.</div><div><br></div><div>So, these two statements:</div><div><br></div><div>cfg1=cfg;<br>
cfg1.baselinewindow = [-seg_window(1) 0 ];<br>
cfg2=cfg;<br>
cfg2.baselinewindow = [0 0.1];</div><div><br></div><div>are basically identical, as the interval -0.1 to 0 (cfg1) and 0 to 0.1 (cfg2) will both contain no data.</div><div><br></div><div>Please double check this with the seg_window set to [-0.1 1]</div><div><br></div><div>Hope that helps,</div><div><br></div><div>Julian<br></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jan 17, 2019 at 2:29 PM Marion Vincent <<a href="mailto:marion.vincent@univ-lille.fr">marion.vincent@univ-lille.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Stephen,<br>
Here is my script:<br>
%segmentation<br>
seg_window=[0.1 1]; % in seconds %preStim/postStim<br>
%config<br>
cfg= [];<br>
cfg.dataset = filename_Data;<br>
%% *********** TRIAL DEFINITION PART *********** (that works)<br>
[…]<br>
cfg = ft_definetrial(cfg);<br>
% *********** Re-References *********** (that also works)<br>
cfg.reref = 'yes';<br>
cfg.refchannel = {'EXG3', 'EXG4'};% electrode 131/132 // cell-array with new EEG reference channel(s), this can be 'all' for a common average reference<br>
cfg.refmethod = 'avg'; % 'avg', 'median', or 'bipolar' for bipolar derivation of sequential channels (default = 'avg')<br>
data_Raw = ft_preprocessing(cfg);<br>
%% *********** Baseline ***********<br>
cfg.demean = 'yes';<br>
cfg1=cfg;<br>
cfg1.baselinewindow = [-seg_window(1) 0 ];<br>
cfg2=cfg;<br>
cfg2.baselinewindow = [0 0.1];<br>
cfg3=cfg;<br>
cfg3.baselinewindow = 'all';<br>
data1 = ft_preprocessing(cfg1);<br>
data2 = ft_preprocessing(cfg2);<br>
data3 = ft_preprocessing(cfg3);<br>
I’ve attached the figure with the results.<br>
PS: In fact I made a mistake in my previous email: the result wasn’t the same when the Baseline window was ‘all’.<br>
Let me know if you need more informations.<br>
Thanks for your help.<br>
Marion<br>
Marion VINCENT<br>
Eng., PhD , CNRS Research Engineer<br>
Tel: +33 607 59 46 76<br>
Laboratoire SCALab UMR CNRS 9193<br>
Université Lille 3<br>
BP 60149<br>
59653 Villeneuve d'Ascq Cedex<br>
<a href="http://scalab.cnrs.fr" rel="noreferrer" target="_blank">http://scalab.cnrs.fr</a><br>
--------------------------------------------<br>
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De: Stephen Whitmarsh<br>
Envoyé le:jeudi 17 janvier 2019 11:51<br>
À: 'FieldTrip discussion list'<br>
Objet:Re: [FieldTrip] Baseline removal errors in trials preprocessing<br>
<br>
<br>
Dear Marion,<br>
<br>
<br>
<br>
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?<br>
<br>
<br>
<br>
Cheers,<br>
<br>
Stephen<br>
<br>
<br>
<br>
From: fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>> On Behalf Of Marion Vincent<br>
Sent: Thursday, January 17, 2019 10:37 AM<br>
To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Baseline removal errors in trials preprocessing<br>
<br>
<br>
<br>
Dear FIeldtrip users, <br>
<br>
<br>
<br>
I’m new in using Fieldtrip for EEG processing and I’ve encountred some issues while removing the Baseline of my trials. <br>
<br>
<br>
<br>
I’m working on EEG signals recorded with the BioSemi system. My pre-processing method is : <br>
<br>
(1) Re-referecing the channels (necessary with BioSemi)<br>
<br>
(2) Trial definition<br>
<br>
(3) Baseline removal<br>
<br>
<br>
<br>
I’ve read on the documentation that ft_preprocessing xcan have several cfg parameter for the Baseline removal :<br>
<br>
<br>
<br>
% cfg.demean = 'yes';%'no' or 'yes', whether to apply baseline correction (default = 'no')<br>
<br>
% cfg.baselinewindow = 'all';%[begin end] ;%in seconds, the default is the complete trial (default = 'all')<br>
<br>
% cfg.detrend = 'no'; %'no' or 'yes', remove linear trend from the data (done per trial) (default = 'no')<br>
<br>
<br>
<br>
I wanted to remove a Baseline defined as the average of a given window preceeding my stimulus onset. <br>
<br>
<br>
<br>
I tried to use : cfg.baselinewindow = [-0.5 0 ]; cfg.baselinewindow = [0 0.1] or the default window .<br>
<br>
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. <br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
Do you have any advice ?<br>
<br>
<br>
<br>
Thanks ! <br>
<br>
Marion<br>
<br>
<br>
<br>
Marion VINCENT<br>
Eng., PhD , CNRS Research Engineer<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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</blockquote></div>