[FieldTrip] Question about MVPA topographic map

D.Abdallah da401 at kent.ac.uk
Tue Sep 19 06:25:36 CEST 2017

Dear all,

I've had a bit of trouble understanding the results that I get when using the ft_topoplotER.

I have run on matlab R2014a the MVPA tutorial on fieldtrip: http://www.fieldtriptoolbox.org/tutorial/multivariateanalysis and tried to understand the resulting topographic map but wasn't able to because there is no proper legend that explains where the x and y axes are and they represent.

The experiment that my supervisor and I conducted is meant to look at the pattern of activity in the brain (using EEG) in a switch vs. non-switch task of Rubin's Face-Vase ambiguous stimulus. In order to study that we are using MVPA.

This is the code we are running on one of the subjects that we collected:


%Reading the data

cfg = [];

cfg.dataset = filename1;

cfg.reref ='yes';

cfg.channel = {'Cz','PO9','PO7','PO3','PO','PO4','PO8''PO10','O1','Oz','O2','O9','O10'};

cfg.refchannel ='Cz';

cfg.demean ='yes';

data_eeg1 = ft_preprocessing(cfg);

%Segmenting data

cfg.trialdef.eventtype ='?';

Dummy = ft_definetrial(cfg);

cfg.trialdef.prestim = 0.1;

cfg.trialdef.poststim = 0.6;

cfg.baselinewindow = [-0.1 0];

cfg.trialdef.eventtype ='STATUS';

cfg.trialdef.eventvalue = [100];

stimulusTrigger = ft_definetrial(cfg);

cfg.trialdef.eventvalue = [1];

FaceTrials = ft_definetrial(cfg);

cfg.trialdef.eventvalue = [2];

VaseTrials = ft_definetrial(cfg);

%Definitions of Triggers

stimulusTrigger = 100;

faceResponseTrigger = 1;

vaseResponseTrigger = 2;

%Define Face Trials and Conduct Preprocessing

[trlFaces, eventFaces] = ft_trialfun_BasedOnResp(FaceTrials,stimulusTrigger,faceResponseTrigger);

hdr = ft_read_header(cfg.dataset);

event = ft_read_event(cfg.dataset);

FaceData = ft_preprocessing(FaceTrials);

FaceTrigger = [eventFaces(strcmp(cfg.trialdef.eventtype, {eventFaces.type})).value]';

FaceSample = [eventFaces(strcmp(cfg.trialdef.eventtype, {eventFaces.type})).sample]';

Facepretrig = -round(cfg.trialdef.prestim * hdr.Fs);

Faceposttrig = round(cfg.trialdef.poststim * hdr.Fs);

%Define Vase Trials and Conduct Preprocessing

[trlVase, eventVase] = ft_trialfun_BasedOnResp(VaseTrials,stimulusTrigger,vaseResponseTrigger);

hdr = ft_read_header(cfg.dataset);

event = ft_read_event(cfg.dataset);

VaseData = ft_preprocessing(VaseTrials);

VaseTrigger = [eventVase(strcmp(cfg.trialdef.eventtype, {eventVase.type})).value]';

Vasesample = [eventVase(strcmp(cfg.trialdef.eventtype, {eventVase.type})).sample]';

Vasepretrig = -round(cfg.trialdef.prestim * hdr.Fs);

Vaseposttrig = round(cfg.trialdef.poststim * hdr.Fs);

%Calculate Face ERP

FaceTrials.reref ='no';

FaceTrials.keeptrials ='yes';% classifiers operate on individual trials

FaceTrials.channel = {'PO9','PO7','PO3','PO','PO4','PO8''PO10','O1','Oz','O2','O9','O10'};% occipital channels only

FaceERP = ft_timelockanalysis(FaceTrials,FaceData);

%Calculate Vase ERP

VaseTrials.reref ='no';

VaseTrials.keeptrials ='yes';% classifiers operate on individual trials

VaseTrials.channel = {'PO9','PO7','PO3','PO','PO4','PO8''PO10','O1','Oz','O2','O9','O10'};% occipital channels only

VaseERP = ft_timelockanalysis(VaseTrials,VaseData);


cfg.layout ='biosemi64.lay';

cfg.method ='crossvalidate';

cfg.design = [ones(size(FaceERP.trial,1),1); 2*ones(size(VaseERP.trial,1),1)];

cfg.nfolds = 4;

cfg.latency = [-0.1 0.6];

cfg.statistic = {'accuracy''binomial''contingency'};

stat = ft_timelockstatistics (cfg, FaceERP,VaseERP);


%Plot MVPA Results

stat.mymodel = stat.model{2}.primal;

cfg.parameter ='mymodel';

cfg.xlim = [-0.1 0.6];

cfg.comments ='';

cfg.colorbar ='yes';



Attached is the resulting topographic map. We found a very weird pattern that doesn't seem to show what we are expecting. It seems as though there might be a glitch or a step we missed.

We came to the conclusion after running figure(imagesc(stat.mymodel)) in order to understand the topographical map and found a completely different pattern (see second attached Imagesc subject 8 file).

Why are the patterns very different?

Moreover, when we ran the MVPA fieldtrip tutorial, the topographical map showed a proper pattern of activity (see tutorial topographic map).

All the best,

Diane Abdallah

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170919/8dfdf20e/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Imagesc Subject 8.fig
Type: application/x-xfig
Size: 40249 bytes
Desc: Imagesc Subject 8.fig
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170919/8dfdf20e/attachment-0004.fig>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Subject 8 Topographical map.fig
Type: application/x-xfig
Size: 450612 bytes
Desc: Subject 8 Topographical map.fig
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170919/8dfdf20e/attachment-0005.fig>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: tutorial topographic map.png
Type: image/png
Size: 10419 bytes
Desc: tutorial topographic map.png
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170919/8dfdf20e/attachment-0002.png>

More information about the fieldtrip mailing list