[FieldTrip] missing sample after using ft_componentanalysis with method bsscca

[Schoffelen, J.M. (Jan Mathijs)]

Hi Linda,

I have adjusted ft_componentanalysis, to remove the sampleinfo field from the output in case bsscca is used as method.
This change will be available at the DCCN cluster soon, is alreadly available on the master development branch on github, and will in the release version on github soon.

Best wishes,
Jan-Mathijs


On 6 May 2020, at 11:34, Drijvers, L. (Linda) <l.drijvers at donders.ru.nl<mailto:l.drijvers at donders.ru.nl>> wrote:

Hi Jan-Mathijs,

Thanks for the fast reply. Data is indeed internally consistent.
And I will read that paper in more detail... Thanks!

Best,
Linda

dr. Linda Drijvers | postdoctoral researcher | https://cosilab.org<https://cosilab.org/>
Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL
www.ru.nl/english/people/drijvers-l/<http://www.ru.nl/english/people/drijvers-l/> | https://www.mpi.nl/people/drijvers-linda

From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: woensdag 6 mei 2020 11:18
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] missing sample after using ft_componentanalysis with method bsscca

Hi Linda

Is the data internally consistent after ft_componentanalysis? In other words, does the number of time points per trial (in data.time) match the number of columns in data.trial?

Please note that the bsscca is a poorly maintained corner (and hardly ever used) of the code, so it might need improvement.

Feel free to send us a Pull Request through github for code improvements.

Best,
Jan-Mathijs

PS: bsscca returns ’shorter’ data than the input because of the way the algorithm works, as described in the reference paper.




On 6 May 2020, at 10:23, Drijvers, L. (Linda) <l.drijvers at donders.ru.nl<mailto:l.drijvers at donders.ru.nl>> wrote:

P.S., sorry, mixed things up: data in comp_output.trial have 499 samples, while smps has 500 elements (presumably based on sampleinfo). So key question is: why do the output trials after bsscca have 1 fewer sample than the input trials?

Best,
Linda

dr. Linda Drijvers | postdoctoral researcher | https://cosilab.org<https://cosilab.org/>
Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL
www.ru.nl/english/people/drijvers-l/<http://www.ru.nl/english/people/drijvers-l/> | https://www.mpi.nl/people/drijvers-linda

From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Drijvers, L. (Linda)
Sent: woensdag 6 mei 2020 09:59
To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
Subject: [FieldTrip] missing sample after using ft_componentanalysis with method bsscca

Dear all,

I’m analysing an EEG dataset using MATLAB 2016a + FieldTrip version 20200409.

I am trying to use ft_componentanalysis with cfg.method = ‘bsscca’ (see code):

cfg             = [];
cfg.channel     = 1:length(data_Aclean.label)-2;
cfg.method      = 'bsscca';
cfg.cellmode    = 'yes';
comp_output      = ft_componentanalysis(cfg, data_Aclean);

When I then try to use ft_databrowser with the following code:
    cfg = [];
    cfg.channel = [1:10];
    cfg.viewmode = 'component';
    cfg.layout = 'customlayout.mat';
    ft_databrowser(cfg, comp_output);

I get the following error:

Index exceeds matrix dimensions.

Error in ft_fetch_data (line 199)
    dat(:,ok) = data.trial{utrl}(chanindx,smps);

Error in ft_databrowser>redraw_cb (line 1630)
  dat = ft_fetch_data(opt.orgdata, 'header', opt.hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx,
  'allowoverlap', istrue(cfg.allowoverlap));

Error in ft_databrowser (line 729)
redraw_cb(h);

A closer look at the data shows that while fsample for my data is 500, smps is 499 after running ft_componentanalysis with method bsscca. However, I can solve the error above by running ft_databrowser with comp_output = rmfield(comp_output, 'sampleinfo').

My question is: what causes this discrepancy in smps (why does this one sample go missing)? Any help would be appreciated.

Best wishes,
Linda Drijvers

dr. Linda Drijvers | postdoctoral researcher | https://cosilab.org<https://cosilab.org/>
Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL
www.ru.nl/english/people/drijvers-l/<http://www.ru.nl/english/people/drijvers-l/> | https://www.mpi.nl/people/drijvers-linda

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