[Eeglablist] Reference point location and Cleanline issue

[Deepa Gupta]

Hi Chester,

Sorry for the delayed reply as I got caught up. Below are my
responses/comments in blue to your questions. Hope that helps

Sincerely
Deepa Gupta <https://urldefense.com/v3/__https://www.linkedin.com/in/deepaguptaresearcher/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-Q9LTdWb0$ >
Postdoc Scholar, SCCN <https://sccn.ucsd.edu/>, SDSC <https://www.sdsc.edu/>
, INC <https://inc.ucsd.edu/index.php>, UCSD <https://ucsd.edu/>
Ph.D. , Dr. Choa's Lab <https://urldefense.com/v3/__https://blogs.cs.umbc.edu/choalab/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-Qk75Im4Q$ >, CSEE
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On Sun, Jan 21, 2024 at 11:10 PM chester20080 <chester20080 at yahoo.gr> wrote:

> 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. - okay then yes we are
> seeing harmonics at 50Hz. you may adjust the parameters accordingly.
> consider inputting the parameter in there as [50 100 150] or further
> depending on your Nyquist frequency. Cleanline unfortunately did not
> work, I used it at 50Hz and at 100Hz but it did nothing, the interference
> remains for both frequencies - please consider changing the parameters. I
> tried that along with applying it more than once and it reduced it
> considerably although not completely but enough to work with. 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? - depends on your
> scientific investigation. I can't say here for sure. we can connect to
> discuss or try coming for EEGLAB workshop :) . I guess I don't expect any
> gamma activity at resting state - not necessarily. there is a lot of
> literature suggesting gamma coupled with theta. A random example: Barry,
> Robert J., et al. "Resting-state EEG gamma activity in children with
> attention-deficit/hyperactivity disorder." *Clinical neurophysiology* 121.11
> (2010): 1871-1877.. Alternatively, could I just use a notch for 50Hz (as
> a bandwidth fir @ 48-52Hz)? - Under our senior expert Scott's kind
> supervision, I learned that it (notch filter) could potentially take a lot
> of information out of your EEG data. Under our expert Makoto's kind
> mentorship, I learned that notch filter can take out the line noise.
> Ultimately, post a lot of time-taking thinking, I went with my decision to
> remove the line noise on my data/data given to me with the method that I
> chose as I realized that I am the best closest judge of my scientific data
> and investigation. Basically, post all the advisory, I'd go with the
> final judgment of the investigator who is looking at the data at the
> closest as that person is the one investigating/handling it/your EEG data
> while following the right principles. So, manage that with care and best
> of luck for your EEG fun. cheers.
>
> 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. - I'd
> suggest you to please consider creating an EEGLAB issue about this. 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? - sure. yes. good thought. 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? -
> depends on your data. Ideally, re-referencing once should be okay but you
> could be needing to do it twice in certain situation - hopefully the data
> is not that wierdly bad - in one of my case it sadly was - just depends.
> Another tip, you may have to see data scroll , spectrum etc before and
> after your applied steps and make the final judgment for your final pipeline
> . Keep in mind that re-referencing with a channel (CZ here) would have
> you lose one channel's worth of data whereas that's not the case with
> average re-referencing. So, you could recover the data (here the CZ
> channel's data) by averaging post referencing with CZ channel's data. hope
> that makes sense. please refer to the documentation again that i
> previously provided if still needed.
> https://urldefense.com/v3/__https://eeglab.org/tutorials/05_Preprocess/rereferencing.html__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-QY0j8Y-c$ 
>

>

> Thank you again in advance. - very welcome. all the best. Deepa
> 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://eeglab.org/tutorials/05_Preprocess/rereferencing.html__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-QY0j8Y-c$  and check
> for *Look up locs*
> Basically 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 helps
> Sincerely
> Deepa Gupta <https://urldefense.com/v3/__https://www.linkedin.com/in/deepaguptaresearcher/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-Q9LTdWb0$ >
> Postdoc Scholar, SCCN <https://sccn.ucsd.edu/>, SDSC
> <https://www.sdsc.edu/>, INC <https://inc.ucsd.edu/index.php>, UCSD
> <https://ucsd.edu/>
> Ph.D. , Dr. Choa's Lab <https://urldefense.com/v3/__https://blogs.cs.umbc.edu/choalab/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-Qk75Im4Q$ >, CSEE
> <https://urldefense.com/v3/__https://www.csee.umbc.edu/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-QKDyql7o$ >, UMBC <https://urldefense.com/v3/__https://www.umbc.edu/__;!!Mih3wA!BLObfypm9iQeVY1LfATL1hFE7qbBD6KPkBPTMn7Ju7RUscVWEK23YYTekDigdYOjC6QWCz0IYxRBUg-QPWOXxzc$ >
>
>
> 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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