[Eeglablist] EEGLAB microstate toolbox

[William McGeown]

Hi Daniele,
Thanks for pointing that out! I got the data instead from the footnote at the bottom of the pdf (which links to the source data [raw and preprocessed data]).

I've tried with the data they provide through that link on p14 (that you kindly provided below also) and it replicates the tutorial results as expected.  So, everything is working as it should for me, which is great.

(Not sure what the full set of differences are exactly between the data they provide there and the data available from the original source.
Having a quick look now, in the datasets they provide the channel locations seem to be the same, but they have removed an additional 6 outer electrodes, and the reference is listed as average rather than unknown.

I'll investigate this more to understand the differences, in case they have implications for when I process my own datasets, but with the tutorial datasets they provide themselves everything is working which is great.
Thanks for your help.

Best regards,

Will






________________________________
From: Daniele Scanzi <dsca347 at aucklanduni.ac.nz>
Sent: 08 November 2022 21:39
To: William McGeown <william.mcgeown at strath.ac.uk>
Cc: eeglablist at sccn.ucsd.edu <eeglablist at sccn.ucsd.edu>; andreas.pedroni at uzh.ch <andreas.pedroni at uzh.ch>
Subject: Re: [Eeglablist] EEGLAB microstate toolbox

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Hi Will,

I have just tried out the toolbox last week and I had no issues replicating the results. I cannot see the screenshot you are referring to. However, I noticed that the link you have used to download the data is not the one reported in the paper (page 14), which is this one: https://urldefense.com/v3/__https://archive.compute.dtu.dk/files/public/users/atpo/Microstate__;!!Mih3wA!C_ZtGWS3Wn0EU3M87R70Af-mXMt7yqkPynWzK_PZgSbosRLGbqkUM83zsjeoOHpWAcGadwcQ5G1J037-9Bt5PLsFTKSuR08FBUDI$  <https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Farchive.compute.dtu.dk*2Ffiles*2Fpublic*2Fusers*2Fatpo*2FMicrostate&data=05*7C01*7Cwilliam.mcgeown*40strath.ac.uk*7C55b39f6c3f3b46b4992408dac1d1ad76*7C631e0763153347eba5cd0457bee5944e*7C0*7C0*7C638035404148467813*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=lurKSkQGkG8HUWS*2FlbEaTZ24O3jlcZFu9tdQlVLatVU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!C_ZtGWS3Wn0EU3M87R70Af-mXMt7yqkPynWzK_PZgSbosRLGbqkUM83zsjeoOHpWAcGadwcQ5G1J037-9Bt5PLsFTKSuR_BpgUJi$  >

>From this link you should be able to download the 4 set (and fdt) files.

Hope this helps!

Daniele Scanzi


On Wed, 9 Nov 2022 at 09:47, William McGeown <william.mcgeown at strath.ac.uk<mailto:william.mcgeown at strath.ac.uk>> wrote:
Dear All,
I was hoping someone might be able to help.
I'm really interested in using one of the EEGLAB microstate toolboxes (MST toolbox: https://urldefense.com/v3/__https://github.com/atpoulsen/Microstate-EEGlab-toolbox__;!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I704u2zOAz$<https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fgithub.com*2Fatpoulsen*2FMicrostate-EEGlab-toolbox__*3B!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I704u2zOAz*24&data=05*7C01*7Cwilliam.mcgeown*40strath.ac.uk*7C55b39f6c3f3b46b4992408dac1d1ad76*7C631e0763153347eba5cd0457bee5944e*7C0*7C0*7C638035404148624039*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=igh2Gfffdo7s4beF20rqI131AL0xXiteIQtCKpkKlwc*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!C_ZtGWS3Wn0EU3M87R70Af-mXMt7yqkPynWzK_PZgSbosRLGbqkUM83zsjeoOHpWAcGadwcQ5G1J037-9Bt5PLsFTKSuR08VOA1H$  >  ).

I have been trying to recreate the results detailed in the tutorial (https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/289850v1.full.pdf__;!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I700tGlzHB$<https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.biorxiv.org*2Fcontent*2F10.1101*2F289850v1.full.pdf__*3B!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I700tGlzHB*24&data=05*7C01*7Cwilliam.mcgeown*40strath.ac.uk*7C55b39f6c3f3b46b4992408dac1d1ad76*7C631e0763153347eba5cd0457bee5944e*7C0*7C0*7C638035404148624039*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=OEeTlEZacvR8iwAFhCv8hfV67*2BBHF370A3fYphbYdMA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!C_ZtGWS3Wn0EU3M87R70Af-mXMt7yqkPynWzK_PZgSbosRLGbqkUM83zsjeoOHpWAcGadwcQ5G1J037-9Bt5PLsFTKSuRzd2ZG4C$  >  ), but with little success.
Perhaps the issue is with the datasets that I am downloading or how I am loading them into EEGLAB.
When I segment the microstates and then plot them - the microstates do not look anything like what is in the tutorial pdf, and instead they appear fragmented (see attached screenshot).  This is in contrast to what would be expected according to p19 of the tutorial.

I'm not sure if the issue for me is that after downloading the tutorial data from here: https://urldefense.com/v3/__http://fcon_1000.projects.nitrc.org/indi/cmi_eeg/eeg.html__;!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I70-lQm_ED$<https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2F*2Ffcon_1000.projects.nitrc.org*2Findi*2Fcmi_eeg*2Feeg.html__*3B!!Mih3wA!Fjqn6-wNLWvD4vBBR0hrfsi7-IW0t09v_Of0QP_eDRuTgLmvdkH_3Gg6euhUEsfEJJzrHU07NN7WmVzUbnazA4pa58I70-lQm_ED*24&data=05*7C01*7Cwilliam.mcgeown*40strath.ac.uk*7C55b39f6c3f3b46b4992408dac1d1ad76*7C631e0763153347eba5cd0457bee5944e*7C0*7C0*7C638035404148624039*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=QQigRf3AuLNAqjJNaQ7Ljl0da7LVm21gDLJbqtvFQuc*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!C_ZtGWS3Wn0EU3M87R70Af-mXMt7yqkPynWzK_PZgSbosRLGbqkUM83zsjeoOHpWAcGadwcQ5G1J037-9Bt5PLsFTKSuR1MfGafj$  >   that the channels are not being set up properly in eeglab.
I have been simply loading the .mat files into EEGLAB from the subject-level preprocessed folders (as .set files are not available from the website).
I think the channel locations seem to look in accordance to the EGI 128 channel configuration.
I have also experimented by loading in an edited EGI channel file (reduced to the correct number of channels), but again with no luck in replicating the tutorial results.

In the tutorial guide it looks like it may have been possible to download .set eeglab files from that website in the past (although I'm not sure about that). Now, however, the available preprocessed files are in .mat and .csv, but there is no eeglab format .set for download.

I was wondering if anyone else has encountered difficulties replicating the tutorial guide and in particular if anyone has perhaps encountered the same issue as me?  Any idea what I am doing wrong?
I have tried the analysis also going back to the version of EEGLAB that the tutorial was ran on (rather than a recent version).
I have also tried the steps both in the GUI and by using the script provided in the tutorial, but obtain these results.

Relatedly - If anyone has the 4 tutorial .set files and could share them with me please, then I could load them into eeglab to see if the datafiles have been the problem for me, or if there is some greater problem?

Hoping someone can help.

Thank you,

Will



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