[FieldTrip] Baseline removal errors in trials preprocessing

[Julian Keil]

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
>
>
>
>
>
>
>
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