[Eeglablist] Reference point location and Cleanline issue

Tue Jan 23 09:38:47 PST 2024

Hi,

Also, try p-value = 0.05 instead of 0.01. And I believe the CleanLine from the Prep Pipeline has more recent improvements, but that's just something I heard, not seen the code. 

There is also the zapline plugin that might give better results. I don't know if anyone compared them. 

Hope this helps.

Cedric

On Monday, January 22nd, 2024 at 10:22 AM, Tim Curran via eeglablist <eeglablist at sccn.ucsd.edu> wrote:

> Hi Chester,
> I recently tried to use cleanLine and benefitted from the following advice from Makoto in 2016.
> Best,
> Tim
> 
> 
> From: eeglablist-bounces at sccn.ucsd.edumailto:eeglablist-bounces at sccn.ucsd.edu <eeglablist-bounces at sccn.ucsd.edumailto:eeglablist-bounces at sccn.ucsd.edu> on behalf of Makoto Miyakoshi <mmiyakoshi at ucsd.edumailto:mmiyakoshi at ucsd.edu>
> 
> Date: Tuesday, April 5, 2016 at 3:09 PM
> To: Eric HG <erichg2013 at gmail.commailto:erichg2013 at gmail.com>
> 
> Cc: eeglablist <eeglablist at sccn.ucsd.edumailto:eeglablist at sccn.ucsd.edu>
> 
> Subject: Re: [Eeglablist] Question about Cleanline
> Dear Eric,
> 
> First of all, did you apply it on the high-pass filtered data? CleanLine uses EEGLAB's Welch's method for FFT (if I remember correctly) to evaluate the spectrum, so the data needs to be high-pass filtered. See Nima Bigdely-Shamlo's PREP pipeline paper for detail.
> 
> Did you average reference the data? It may help, especially if your data are not re-referenced at all (like Biosemi's data).
> 
> Another thing is that you can expect a small improvement by doing this
> 
> 'SlidingWinLength',4,'SlidingWinStep',4
> 
> If these does not work, I recommend you band-pass filter your data 45-55Hz to see stationarity of your 'line noise'-- is it really it??
> 
> Makoto
> 
> 
> On Fri, Mar 4, 2016 at 2:14 AM, Eric HG <erichg2013 at gmail.commailto:erichg2013 at gmail.com> wrote:
> 
> Hi everybody,
> 
> I've been trying to apply Cleanline instead of a notch filter but there seems to be a problem with some of the subjects. Cleanline doesn't seem to remove all the line noise (at 50 Hz) (see picture). Before I use cleanline I use the function pop_firwsord to high- and low-pass the EEG.
> 
> I use cleanline with the following settings:
> 
> 
> [EEG, Sorig, Sclean, f, amps, freqs, g] = pop_cleanline(EEG, 'Bandwidth',2,'ChanCompIndices',[1:EEG.nbchan], ...
> 
> 'SignalType','Channels','ComputeSpectralPower',true, ...
> 
> 'LineFrequencies',[50] ,'NormalizeSpectrum',false, ...
> 
> 'LineAlpha',0.01,'PaddingFactor',2,'PlotFigures',false, ...
> 
> 'ScanForLines',true,'SmoothingFactor',100,'VerboseOutput',1, ...
> 
> 'SlidingWinLength',4,'SlidingWinStep',2);
> Does anyone know what might need to be changed to fix this?
> 
> Best,
> 
> Eric
> 
> 
> [Inline image 1]
> 
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> 
> 
> From: eeglablist eeglablist-bounces at sccn.ucsd.edu on behalf of chester20080 via eeglablist eeglablist at sccn.ucsd.edu
> 
> Date: Monday, January 22, 2024 at 10:30 AM
> To: Deepa Gupta deepag1 at umbc.edu
> 
> Cc: eeglablist at sccn.ucsd.edu eeglablist at sccn.ucsd.edu
> 
> Subject: Re: [Eeglablist] Reference point location and Cleanline issue
> Thank you for the prompt response.
> 
> I'm in Europe, so the interference here is at multiples of 50Hz and the signal was recorded on the scalp externally. Cleanline unfortunately did not work, I used it at 50Hz and at 100Hz but it did nothing, the interference remains for both frequencies. I forgot to mention that the patient is at resting state and is considered healthy. Perhaps I should low pass at 75Hz or even at 40-50Hz? I guess I don't expect any gamma activity at resting state. Alternatively, could I just use a notch for 50Hz (as a bandwidth fir @ 48-52Hz)?
> 
> For the reference, G2 is not included in the file, in the lookup, so even if I name an additional channel G2 and click on look up locs, it cannot load the coordinates since this point is not a standard besa 4-shell dipfit point I think, and I don't have any locations file to use as source. However, could I use Cz itself as the reference point instead, since G2 (the actual reference point for which I don't have any other data/info) is so close to Cz? And use the procedure described in the link to append another Cz channel only to use it as reference? In case I do just that, do I need to run average re-referencing based on Cz as well or just set Cz as the reference channel in the Channel locations window?
> 
> Thank you again in advance. Στις Δευτέρα 22 Ιανουαρίου 2024 στις 02:45:16 π.μ. EET, ο χρήστης Deepa Gupta deepag1 at umbc.edu έγραψε:
> 
> 
> Hi Chester,
> Thankyou for using EEGLAB. Please see the responses below:
> regarding your query#1 - are you not seeing a harmonic at 60Hz? If not then yes, it could be harmonic. It also depends on where this was recorded. you may preferably consider using cleanline (more than once if needed) among other possible techniques. regarding your query#2 - Please check this if you haven't already: https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Feeglab.org*2Ftutorials*2F05_Preprocess*2Frereferencing.html__*3B!!Mih3wA!EfAh3J2UBkVkGF_y_CzGvue6XCKLeprgZhPzRWRdKZzx25SgLurqW9H5PA_0dwnoF-aKHiUJ07F38M8Qnats3piCaRtNFg*24&data=05*7C02*7Ctim.curran*40colorado.edu*7Cafe750751cbd4b2153d708dc1b6fc9eb*7C3ded8b1b070d462982e4c0b019f46057*7C1*7C0*7C638415414159631317*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=7y*2FLhNYfAtCfZhvqAy6hDrDuqEJvcFPoRi05tsNxIBo*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!HD_n2xGDMuYmp3_Jnl1fqPqkMUZY-FOsnzG52g4fJgKinlr8ZNsDIR-UUGXWx4M5tGtk_NHK4zmYEkYPoGAQr8jIKcJbQA$ https://urldefense.com/v3/__https://eeglab.org/tutorials/05_Preprocess/rereferencing.html__;!!Mih3wA!EfAh3J2UBkVkGF_y_CzGvue6XCKLeprgZhPzRWRdKZzx25SgLurqW9H5PA_0dwnoF-aKHiUJ07F38M8Qnats3piCaRtNFg$ and check for Look up locsBasically you would need to go to Edit -> channel locations - then please append channel as per the documentation if you must followed by Look up locs to get the coordinates for G2 and then have it as set reference. Once that's done, you may re-refer by going to Tools → Re-reference the data
> 
> Hope that helpsSincerely
> Deepa GuptaPostdoc Scholar, SCCN, SDSC, INC, UCSDPh.D. , Dr. Choa's Lab, CSEE, UMBC
> 
> On Sun, Jan 21, 2024 at 2:30 PM chester20080 via eeglablist eeglablist at sccn.ucsd.edu wrote:
> 
> 
> Hello all,
> I am a postgraduate student in biomedical engineering and this is my first time analyzing EEG signals in eeglab. The recording is from a healthy person at resting state. The montage is based on the International 10-20 system and has 19 electrodes (no location file, the locations are automatically recognized with BESA 4shell dipfit). The recording was done with reference to point G2 set 1 cm under Cz at a sampling rate (frequency) of 256 Hz.
> 
> 1) When I plot the spectrum I see two big peaks at 50Hz and 100Hz, while the 100Hz is higher than 50Hz. Is this harmonic power line interference? The problem is that the cleanline plugin does not remove this artifact at all, it does nothing, the interference remains at both frequencies unchanged, unattenuated.
> 
> 2) The second problem is that I don't know how to use the information about the reference point G2 located 1cm under Cz. I have Cz coordinates in both polar and cartesian. "Under" means inside the brain vertically so Z coordinate needs to decrease by 10mm or does it mean externally following the spherical curvature of the head or something, in which case both X and Z change, but then it gets very complicated, what are the exact coordinates for G2? And then I have to create such a channel manually, insert the G2 coordinates and run re-reference? I'm lost.
> 
> Can you please help me? Thank you in advance.
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