[FieldTrip] Warning: copying input chantype to Montage in runica

[Felicitas Huber]

Thank you, yes this was very helpful! You are correct, I am not planning
any source reconstruction.

Best wishes,
Felicitas

On Wed, Feb 2, 2022 at 2:07 AM Schoffelen, J.M. (Jan Mathijs) via fieldtrip
<fieldtrip at science.ru.nl> wrote:

> Hi Felicitas,
>
> I am currently examining peak alpha frequency. To do so, I am analyzing
> EEG data collected during a period of 6 minutes of rest.
>
> Prior to running frequency analysis, I am using PCA to remove non-brain
> artifacts.
>
>
> I assume that you mean ICA, rather than PCA, given the cfg details you
> pasted below in your original e-mail.
>
> While the algorithm seems to work, I am getting the following warning:
>
> “*Warning: copying input chantype to montage.”*
>
> The script still runs, but I wanted to make sure I understand what
> fieldtrip is doing. I am importing the data from eeglab. Below my code:
>
>         cfg = [];
>         cfg.dataset = 'epoched_closed.set'; %this is the dataset
>         ft_data1 = ft_preprocessing(cfg);
>         cfg.length=5;
>         cfg.overlap=0;
>         data=ft_redefinetrial(cfg,ft_data1);
>         cfg.method       = 'runica';
>         cfg.runica.pca=15;
>        * X=ft_componentanalysis(cfg,data); *%%this is the line that gives
> me the warning
>
>
> As a recommendation, I suggest to start off with a ‘fresh’ cfg prior to
> calling ft_componentanalysis, to avoid unwanted side effects of defined
> options from a previous analysis step.
>
> The warning can be ignored. Background: the component unmixing that is
> achieved by ft_componentanalysis reflects a linear projection of the
> original channel data. In order to keep the data object consistent with
> itself, i.e. to keep the ‘description’ of the electrodes consistent with
> what is in the time series, the same linear projection needs to be applied
> to the data object’s ‘elec’-field. Along with the linear projection, the
> specification of the channeltype changes from ‘eeg’ to something
> potentially ill-defined (to something that is not easily defined as
> something that reflects a physical detector). Why once upon a time this
> change in chantype was deemed sufficiently relevant in order for it to
> deserve a warning, I don’t know. By the way, Fieldtrip’s attempt to keep
> the electrode description consistent with the time series would be relevant
> in case you would consider source reconstruction at a later stage of the
> analysis. Given your research question, I assume that this is not im Frage
> (and even if it were, it wouldn’t be recommended given the low number of
> electrodes).
>
> I hope this clarifies things.
>
> Best wishes,
> Jan-Mathijs
>
>
>
>
>
>
> The cfg and data I use are as follows:
>
> cfg =
>     dataset: 'epoched_closed.set'
>      length: 5
>     overlap: 0
>      method: 'runica'
>      runica: [1×1 struct]
>
> data =
>          label: {31×1 cell}
>        fsample: 500
>           elec: [1×1 struct]
>            cfg: [1×1 struct]
>            hdr: [1×1 struct]
>          trial: {1×36 cell}
>           time: {1×36 cell}
>     sampleinfo: [36×2 double]
>
> I have looked into the warning and am assuming "chantype" lets fieldtrip
> know that it is handling eeg data, but would appreciate some more insight
> into what fieldtrip is doing behind the scenes (i.e., why the warning pops
> up).
>
> Thank you,
> Felicitas
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8g-CuxoZMze_QrAXgZwKnmLE5UwNBmNxUN1aoKBsS1LPEkIZUoSR6TyF1V2HgqisgAEA5k6SO3wh8vne3BVKDITsq5D5TrLGJ8AVHw$
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>


-- 
*Felicitas A. Huber, M.A.*
Doctoral Student, Clinical Psychology
Research Assistant, Psychophysiology Laboratory of Affective Neuroscience
The University of Tulsa
https://artsandsciences.utulsa.edu/psychophys/
*918-631-3565*; *918-631-2175*
feh9986 at utulsa.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20220203/2424feb0/attachment.htm>