[Eeglablist] Info on tools for Representational similarity of EEG data in sensor domain (Nike gnanateja)

[Andreea Ioana Sburlea]

 Hi Nike,

For an example, please see this paper: Sburlea, Andreea I., and Gernot R.
Müller-Putz. "Exploring representations of human grasping in neural, muscle
and kinematic signals." *Scientific reports* 8.1 (2018): 1-14.
For the analysis, I used custom made code in Matlab and some of the
functions from the following toolbox: Nili, Hamed, et al. "A toolbox for
representational similarity analysis." *PLoS computational biology* 10.4
(2014).
Hope this helps!

Best,
Andreea Sburlea

On Thu, Apr 30, 2020 at 9:00 PM <eeglablist-request at sccn.ucsd.edu> wrote:

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> Today's Topics:
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>    1. Info on tools for Representational similarity of EEG      data in
>       sensor domain (Nike gnanateja)
>    2. Re-referencing & channel names (Curtis Bingham)
>    3. Problems with editing STUDY design (marco mcsweeney)
>    4. Re: Re-referencing & channel names (Tarik S Bel-Bahar)
>
>
>
> ---------- Forwarded message ----------
> From: Nike gnanateja <nikegnanateja at gmail.com>
> To: eeglablist at sccn.ucsd.edu
> Cc:
> Bcc:
> Date: Wed, 29 Apr 2020 13:13:34 -0400
> Subject: [Eeglablist] Info on tools for Representational similarity of EEG
> data in sensor domain
> Dear List
>
> I am looking for a toolbox or scripts for representational similarity
> analysis (RSA) of EEG data. I don't have anatomical data, so I want to
> explore RSA in the sensor domain only. Is anyone familiar with such tools
> that can operate well in the sensor domain? Any leads would be greatly
> appreciated.
>
> Best
> Nike
>
>
>
>
> ---------- Forwarded message ----------
> From: Curtis Bingham <cnbingham at gmail.com>
> To: <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Wed, 29 Apr 2020 14:23:46 -0700
> Subject: [Eeglablist] Re-referencing & channel names
> Folks,
> Must you re-reference to perform ICA?
> And if so, how do you re-reference to linked-ears?
> How do you change the channel labels from a dataset?
>
>
> 1.) We’re getting up to speed using eeglab. We’re recording in 19 channels
> with a linked-ears reference. The tutorials and Arnaud’s video overviews
> talk about re-referencing regularly. Must you re-reference to perform ICA?
> If the data were collected using linked-ears is there any reason to
> re-reference the data, assuming we’re not examining a very localized
> trouble-spot?  Or can the data be used as-is, without re-referencing?
>
>
>
> 2.) If we must re-reference, how do you do so with linked-ears?  Are A1 &
> A2 equivalent to T9 & T10? The literature shows an average reference is
> inaccurate unless you have very high-density coverage (i.e. more than 19
> channel cap). We don’t yet have the understanding to do REST. Is it
> sufficient to manually create two new channels in our data via the Channel
> Locs window to represent mastoid placement, and modify the channel locs
> (.ced) file to append to it the dimensions for T9 & T10? Or is there an
> equivalent polar dimension for A1 & A2?
>
>
>
> 3.) How do you change the channel labels from a dataset? We’re recording
> with a NeuroField Q20 19-channel device. The output EDF file names channels
> with prefix & suffix that need to be modified before channel locations are
> set. Names are of the format EEG-ZZ-LE, where ZZ=traditional 10-20 sites.
> Presently we’re manually deleting both EEG- prefix and -LE suffix and it is
> time-consuming. Is there an easy way to pre-process the EDF file to strip
> these extra characters?
>
>
>
>
>
>
>
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: marco mcsweeney <marcomcsweeney at gmail.com>
> To: eeglablist at sccn.ucsd.edu
> Cc:
> Bcc:
> Date: Thu, 30 Apr 2020 13:32:36 +0100
> Subject: [Eeglablist] Problems with editing STUDY design
> Hi all,
>
> I have a quick question regarding STUDY design. When I open the edit STUDY
> design popup menu, many of the fields are not displayed. First I thought
> that maybe this was a result of the way I entered the data when I created
> the study but after trying to enter the data in a number of different ways
> i.e. loading a single .set file per participant or entering 3 .set files
> per participant per condition,I still only see a limited number of
> fields/options. Please see attached figure.....
>
> To make sure that it wasn't something I was doing wrong, I downloaded the
> 5sample data from the eeglab wiki and found the same issue with this study
> also. I am using eeglab  v2019.0 running on Matlab R2019b. Could this be a
> compatibility issue or is there a way to edit the pop_studydesign.m
> function or is this just a new GUI?
>
> Any help or advice would be greatly appreciated!
>
> Best wishes
>
>
>
>
> ---------- Forwarded message ----------
> From: Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
> To: Curtis Bingham <cnbingham at gmail.com>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Bcc:
> Date: Thu, 30 Apr 2020 12:53:56 -0400
> Subject: Re: [Eeglablist] Re-referencing & channel names
> Hi Curtis, brief notes below that may be useful. Cheers.
>
>
> *********************************************************
> Not necessary (but often suggested) to reref before ICA. There are several
> camps of preferences about rereferencing before/after ICA.
> Recommendation would be to go with recent pubs in high-quality journals
> using ICA-19-EEG, Then at least your choice is defendable by published
> precedent.
>
> Consider also CSD/Laplacian (though not often used in conjunction with
> ICA), and yes, keep remembering the limitations of average reference and/or
> ICA for low-density-EEG (< ~40-60 channels). Things may get better in the
> future for low-density-EEG with better methods and tech. Yes, definitely,
> 19-chan data certainly give much less valid and fewer neural ICs. However
> 19-chan data, in practice, does give up at least a few interpretable good
> ICs, especially when the data is high-quality. Some researchers only use
> ICA for low-density-EEG to remove clearly artifactual ICs (e..g, eye,
> muscle, and zombie ICs).
>
> You should be okay with linked-ears only as recorded.  Check if previous
> teams published linked-ears 19-chan ICA without further referencing in good
> or high-quality journals.
> There's certainly a wide range of 19-chan ICA papers out there, including
> in higher-quality journals (easy to googlescholar).
>
> One could do test with a few files to see the differences if any, or report
> on two or more referencing schemes (and their effect on study effects).
> So in brief, a few in-house tests comparing a few approaches might be the
> best thing here.
>
> Would advise caution if creating new channels and then using them for some
> referencing procedure.
>
> Some channel renaming suggestions below.
> In brief the labels are addressable and modifiable via matlab script in a
> loop that acts on each .set file
> that you would like to modify (rather than modify the EDFs themselves), or
> do the manual editing of info.
>
> way 1?
> import a new channel .txt file that
> *save out the current channel locations via eeglab gui Channel Editor) -
> from a loaded EDF file with the messed up channel labels
> *edit/save the channel locations file in a text editor
> *import the new channel locaitons file in a loop that opens, changes, and
> saves each .set file
>
> way 2?
> in a loop through that opens each .set file....
> *loop through the EEG.chanlocs.labels
> *find labels that contain (contains matlab function) strings you don't want
> and replace/delete (strrep matlab function) those substrings
> *update/save the EEG structure and .set file
>
> way 3?
> *Go into one file's EEG.chanlocs structure. Get the labels column. Save as
> new cell array of strings.
> *Edit the cell array of channel labels
> *Then apply it, via code, into the first column of EEG.chanlocs, and
> update/save EEG structure.
>
>
> * if you haven't had a chance to, check eeglab scripting wiki, and makoto
> suggestions page, for a range of useful info that may be of use
> *********************************************************
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 3:56 AM Curtis Bingham <cnbingham at gmail.com>
> wrote:
>
> > Folks,
> > Must you re-reference to perform ICA?
> > And if so, how do you re-reference to linked-ears?
> > How do you change the channel labels from a dataset?
> >
> >
> > 1.) We’re getting up to speed using eeglab. We’re recording in 19
> channels
> > with a linked-ears reference. The tutorials and Arnaud’s video overviews
> > talk about re-referencing regularly. Must you re-reference to perform
> ICA?
> > If the data were collected using linked-ears is there any reason to
> > re-reference the data, assuming we’re not examining a very localized
> > trouble-spot?  Or can the data be used as-is, without re-referencing?
> >
> >
> >
> > 2.) If we must re-reference, how do you do so with linked-ears?  Are A1 &
> > A2 equivalent to T9 & T10? The literature shows an average reference is
> > inaccurate unless you have very high-density coverage (i.e. more than 19
> > channel cap). We don’t yet have the understanding to do REST. Is it
> > sufficient to manually create two new channels in our data via the
> Channel
> > Locs window to represent mastoid placement, and modify the channel locs
> > (.ced) file to append to it the dimensions for T9 & T10? Or is there an
> > equivalent polar dimension for A1 & A2?
> >
> >
> >
> > 3.) How do you change the channel labels from a dataset? We’re recording
> > with a NeuroField Q20 19-channel device. The output EDF file names
> channels
> > with prefix & suffix that need to be modified before channel locations
> are
> > set. Names are of the format EEG-ZZ-LE, where ZZ=traditional 10-20 sites.
> > Presently we’re manually deleting both EEG- prefix and -LE suffix and it
> is
> > time-consuming. Is there an easy way to pre-process the EDF file to strip
> > these extra characters?
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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