[FieldTrip] manually adding channel info and reference

[Roy Cox]

thank you Julian,

that was helpful.

Roy

On Mon, Jun 7, 2021 at 11:44 AM Julian Keil via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Hi Roy,
>
> without going into details, and from the top of my head some thoughts:
>
> @1: Why do you need the other channel types in the topo? Would it make
> more sense to plot them separately? In that case, you can use a selection
> with cfg.channel for the desired channels in the plot function (or any
> other function).
>
> @2: I guess there aren’t any restrictions. There are some conventions for
> the MEG gradiometers and magenetometers (see e.g. here:
> https://www.fieldtriptoolbox.org/reference/ft_chantype/).
>
> @3: As before, I think you can specify the reference channel array. For
> example, if you want to re-reference channels 1:256 to the average
> reference, you could set cfg.refchannel = 1:256 in ft_preprocessing.
> Although in that case all channels will be referenced to the average of
> 1:256. For more refined referencing choices, ft_apply_montage might be more
> appropriate: https://www.fieldtriptoolbox.org/reference/ft_apply_montage/ ,
> or keeping the two datasets apart until the referencing is done might be
> easier.
>
> Best,
>
> Julian
>
> Am 01.06.2021 um 13:47 schrieb Roy Cox via fieldtrip <
> fieldtrip at science.ru.nl>:
>
> hello,
>
> I'm having some trouble specifying several kinds of EEG recording
> details/metadata required for further processing. From looking at
> tutorials, functions, and the mailing list, it appears that Fieldtrip
> usually determines these things cleverly from the input data, but in my
> case this information needs to be manually added.
>
> DATA
> My data are 8-h continuous 265-channel signals in Brainvision format (256
> "active" EEG channels, the implicit EEG reference [Cz, flatline], and 8
> bipolar physiological signals). Data were originally recorded in EGI's mff
> format, but have since been downsampled and converted to Brainvision (no
> doubt resulting in some loss of metadata).
>
> After reading data into Fieldtrip, I'm left with this bare-bones structure:
>
> data_ft =
>
>   struct with fields:
>
>     fsample: 250
>       trial: {[265×7671535 single]}
>        time: {[1×7671535 double]}
>       label: {1×265 cell}
>         cfg: [1×1 struct]
>
>
> Basically the data and channel labels (as present in the Brainvision
> file), nothing more.
>
> ELECTRODE LOCATIONS
> I get my EEG electrode coordinates from reading the header of one of the
> original mffs:
>
> hdr_mff = ft_read_header(mff_file)
> elec_eeg=hdr_mff.elec
>
> elec_eeg =
>
>   struct with fields:
>
>      chanpos: [257×3 double]
>     chantype: {257×1 cell}
>     chanunit: {257×1 cell}
>      elecpos: [257×3 double]
>        label: {257×1 cell}
>         type: 'egi256'
>         unit: 'cm'
>
>
> So this reflects the 256+1 EEG electrodes, but not the physiological
> signals (presumably because the mff file doesn't - and couldn't - hold this
> information). I can turn these EEG coordinates into an EEG layout that
> looks accurate (and very similar to the EGI template layout provided in
> Fieldtrip):
>
> cfg = [];
> cfg.elec = elec_eeg;
> mff_layout = ft_prepare_layout(cfg);
> figure
> ft_plot_layout(mff_layout);
>
>
> So far so good.
>
> Q1: how do I add (mock) location information for the bipolar phys signals?
> I imagine I'll run into trouble if channel/electrode counts don't match
> between ft_data and elec_eeg. It would also be nice to be able to create a
> layout that includes the phys signals (which means they should be present
> in the elec_eeg struct). Do I manually expand the elec_eeg fields from 257
> to 265? Suggestions for mock values that work well with ft_prepare_layout?
>
> CHANNEL TYPES
> Q2: how/where do I specify that the 8 phys channels are not EEG? Can
> elec_eeg.chantype be set to "non-eeg" or even more specific types (e.g., we
> have ecg, emg, etc..)? I can't find an overview of allowed channel types.
> And is it only the elec_eeg structure that needs this info, or do I need to
> specify it elsewhere too? (Ultimately, I'd like to be able to use
> ft_selectdata to select specific channel types etc.)
>
> REFERENCE
> Q3: how/where do I indicate that the first 256 channels are referenced to
> channel 257 (Cz, which is flatline), and that channels 258-265 are bipolar
> channels, such that later re-referencing works as intended? (I know having
> the EEG refence channel explicitly in the data is uncommon, so perhaps it
> needs to be deleted?)
>
> Thanks for any input!
>
> Best,
> Roy
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20210614/90291938/attachment.htm>