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

[Helena Pereira]

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
>> >
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > fieldtrip mailing list
>> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> > https://doi.org/10.1371/journal.pcbi.1002202
>>
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>>
>
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