[FieldTrip] Can the warning "Warning: could not determine dimord of "comp" in:" influence the results?

[Helena Pereira]

Thank you very much, Eelke.

Best,
Helena

Eelke Spaak <e.spaak at donders.ru.nl> escreveu no dia terça, 9/06/2020 à(s)
12:59:

> Dear Helena,
>
> Yes, you can safely ignore the warning.
>
> Best,
> Eelke
>
> On Tue, 9 Jun 2020 at 12:14, Helena Pereira
> <hri.pereira at campus.fct.unl.pt> wrote:
> >
> > Dear Eelk,
> >
> > Perhaps everything is ok, and I can ignore the warning. The structure of
> my data is as follows (and contains the components that you mentioned: e.g.
> .topolabel), or it should also appear in the component analysis?
> >
> > ica_cleaned =
> >   struct with fields:
> >        fsample: 512
> >           time: {1×100 cell}
> >          trial: {1×100 cell}
> >           topo: [69×69 double]
> >       unmixing: [69×69 double]
> >          label: {69×1 cell}
> >      topolabel: {69×1 cell}
> >     sampleinfo: [100×2 double]
> >      trialinfo: [100×1 double]
> >            cfg: [1×1 struct]
> >
> > Thank you for your time and help.
> >
> > Best,
> > Helena Pereira
> >
> >
> > Helena Pereira <hri.pereira at campus.fct.unl.pt> escreveu no dia terça,
> 9/06/2020 à(s) 09:38:
> >>
> >> Dear Eelk,
> >>
> >> Yes, 'ica_cleaned' is produced directly from ft_componentanalysis:
> >>
> >> cfg = [];
> >> cfg.dataset=subject;
> >> cfg.trialfun = 'ft_trialfun_general'; % this is the default
> >> cfg.trialdef.eventtype  = 'Stimulus';
> >> cfg.trialdef.eventvalue ={Stimulus}';
> >> cfg.trialdef.prestim    = 2; %latency in seconds
> >> cfg.trialdef.poststim   = 2; %latency in seconds
> >> cfg=ft_definetrial(cfg);
> >>
> >> cfg.channel = [1:69]; %discard channels not used
> >> cfg.preproc.reref = 'yes';
> >> cfg.preproc.refchannel = {'M1' 'M2'}; %avg mastoids
> >> cfg.continuous = 'yes';
> >> cfg.preproc.detrend = 'no';
> >> %Baseline correction
> >> %cfg.preproc.demean = 'yes';
> >> cfg.prepoc.baselinewindow  = [-0.2 0];
> >> %Filtering
> >> cfg.preproc.lpfilter = 'yes';
> >> cfg.preproc.hpfilter = 'yes';
> >> cfg.preproc.lpfreq = 100;
> >> cfg.preproc.hpfreq = 1;
> >> data=ft_preprocessing(cfg);
> >>
> >> cfg = [];
> >> cfg.method = 'runica';
> >> cfg.demean = 'yes';
> >> ica_cleaned = ft_componentanalysis(cfg,data);
> >>
> >> % %Save ICA data
> >> % outfile=strcat(save_dir,'/',infile,'_', sti,'.mat')
> >> % save(outfile, 'ica_cleaned', '-v7.3')
> >>
> >> cfg = [];
> >> cfg.component = 1:20;
> >>
> >> cfg.layout = 'biosemi64.lay';
> >> cfg.comment   = 'no';
> >> figure();
> >> ft_topoplotIC(cfg,ica_cleaned)
> >>
> >> The data is in the BrainVision Format ( .vhdr, .vmrk and .seg),
> obtained as suggested by Fieldtrip website:
> http://www.fieldtriptoolbox.org/getting_started/brainvision/
> >>
> >> Can I ignore the Warning?
> >>
> >> Best,
> >> Helena Pereira
> >>
> >> Eelke Spaak <e.spaak at donders.ru.nl> escreveu no dia terça, 9/06/2020
> à(s) 08:15:
> >>>
> >>> Dear Helena,
> >>>
> >>> In general, you can probably safely ignore the warning. It just means
> >>> that FieldTrip is unsure of the dimensionality of the 'comp' field,
> >>> because there is no 'compdimord' and also the dimensionality does not
> >>> match the data in any straightforward way.
> >>>
> >>> However, the structure of your componentanalysis output is somewhat
> >>> strange. From .topo and .unmixing, it appears there is only one
> >>> component. However, .label has 69 elements, and there is no .topolabel
> >>> (which usually is there). Is the output you posted directly produced
> >>> by ft_componentanalysis (i.e. it is the 'ica_cleaned' variable
> >>> immediately after the step you showed)?
> >>>
> >>> Best,
> >>> Eelke
> >>>
> >>> On Mon, 8 Jun 2020 at 21:42, Helena Pereira
> >>> <hri.pereira at campus.fct.unl.pt> wrote:
> >>> >
> >>> > Dear FieldTrip users,
> >>> >
> >>> > I'm running the ft_componentanalysis function after applying ICA to
> my data. Although I'm not getting any error, the following warning came out:
> >>> >
> >>> > Warning: could not determine dimord of "comp" in:
> >>> >
> >>> >              label: {69×1 cell}
> >>> >                cfg: [1×1 struct]
> >>> >               topo: [69×1 double]
> >>> >         topodimord: 'chan_comp'
> >>> >               comp: 7
> >>> >           unmixing: [1×69 double]
> >>> >     unmixingdimord: 'chan_topochan'
> >>> >
> >>> > Can this influence the way the components are displayed and
> consequently my results? Is this associated with the layout that I used or
> with the "demean" option?
> >>> >
> >>> > My code is as follows:
> >>> > cfg = [];
> >>> > %cfg.channel = 1:64;
> >>> > cfg.method = 'runica';
> >>> > cfg.demean = 'yes';
> >>> > ica_cleaned = ft_componentanalysis(cfg, data);
> >>> >
> >>> > cfg = [];
> >>> > cfg.component = 1:20;
> >>> > cfg.layout = 'biosemi64.lay';
> >>> > cfg.comment   = 'no';
> >>> > ft_topoplotIC(cfg, ica_cleaned )
> >>> >
> >>> > Thanks in advance,
> >>> > Keep safe,
> >>> > Helena Pereira
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
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> >>> > https://doi.org/10.1371/journal.pcbi.1002202
> >>>
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> >
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