[Eeglablist] high frequency oscillation- eeg advice

Thu Jan 26 15:36:04 PST 2017

Dear Jumana,

When you do the bandpass at once, the filter order for 0.1Hz high-pass will
be applied to your low-pass, which should be really excessive. It's better
to do high-pass and low-pass separately. And I still don't like 0.1Hz
high-pass if you use FIR (and I do not know how bad it is to use IIR...
I've heard it can become 'unstable' but I've never seen it myself)

> I won't be using granger causality but I will be estimating phase during
ITC.

Should be ok.

Makoto

On Thu, Jan 26, 2017 at 2:12 PM, Ahmad, Jumana <jumana.ahmad at kcl.ac.uk>
wrote:

> Dear Makoto,
> I actually switched to the pop eeg filt eeglab function and it now Really
> attenuated anything >40Hz, and my ERPs are cleaner. However I filtering
> between 0.1-40Hz at the same time in the GUI (I interned the high pass and
> low pass simultaneously). Is this OK to do? The frequency response looks
> OK.
>
> The filter order was automatically set very high by the GUI, but it's
> continuous data and I have room without events at the beginning and end of
> the data so any edge effects can be disgusted. What do you think?
>
> Also, this is for my ERP analysis- I trained ICA on a 1Hz high pass
> filtered set.
> I won't be using granger causality but I will be estimating phase during
> ITC.
> Best wishes, and thanks,
> Jumana
>
> ------------------------------------------
> Jumana Ahmad
> Post-Doctoral Research Worker in Cognitive Neuroscience
> EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study
> Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23)
> | Institute of Psychiatry, Psychology & Neuroscience | King’s College
> London | 16 De Crespigny Park | London SE5 8AF
>
> Phone: 0207 848 5359| Email: jumana.ahmad at kcl.ac.uk | Website:
> www.eu-aims.eu | Facebook: www.facebook.com/euaims
>
> ------------------------------
> *From:* Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> *Sent:* 26 January 2017 23:49:50
> *To:* Ahmad, Jumana
> *Cc:* eeglablist at sccn.ucsd.edu
> *Subject:* Re: [Eeglablist] high frequency oscillation- eeg advice
>
> Dear Jumana,
>
> It's a bad idea to perform ICA with 0.1Hz high-pass filtered data. The
> cutoff frequency is too low. See this page and the referenced paper.
>
> https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_
> pipeline#High-pass_filter_the_data_at_1-Hz_.28for_ICA.2C_
> ASR.2C_and_CleanLine.29
> <https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsccn.ucsd.edu%2Fwiki%2FMakoto%2527s_preprocessing_pipeline%23High-pass_filter_the_data_at_1-Hz_.28for_ICA.2C_ASR.2C_and_CleanLine.29&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C35190d19320946ffd52408d446355d20%7C8370cf1416f34c16b83c724071654356%7C0&sdata=XQPtEZ22iFzlB2PVii2GjBWVdfPOZZnmnmOfGa8CbgI%3D&reserved=0>
>
> > A 30Hz low pass does not help to get rid of the oscillation, which is
> really significant in the data.
>
> Check the channel frequency spectra and tell me if you see peaks in it. If
> necessary, you can cut it off using a designed low-pass filter (not like
> Butterworth...)
>
> > I use a butterworth filter, which is good for ERP analysis with low
> phase distortion.
>
> Do not make qualitative judgement just because something is NOT a classic
> Butterworth. Of course, if the attenuation is small, the phase 'distortion'
> is small. But if such small attenuation is not useful, it does not help at
> all! Also, be careful with the word 'phase'. Particularly people who do not
> know basics of signal processing believe phase as some magical thing. If
> you are not performing Granger Causality Analysis or something, you don't
> need to be so worried about phase issue in practice.
>
> > I also already run ICA, but in some datasets there is a very significant
> high frequency oscillation.
>
> Remember, to eliminate this is more important than being afraid of
> qualitative phase issue.
>
> > However, I can see the high frequency oscillations in my ERP, which is
> not ideal and now I need to try and get rid of it further.
>
> Can I filter again on top of the data which already has already undergone
> ICA- I only use ICA to remove blinks?
>
> You'd better to filter the data on continuous state. If you need to filter
> the epoched data, the half of filter length from both ends becomes
> unreliable.
>
> > Should I do cleanline, although it would have to be after ICA now- I
> read this is not advisable.
>
> > Should I use a notch filter?
>
> If you see > 20dB line noise, Cleanline may not help. In this case, I
> would simply apply a designed low-pass filter, either Hamming (-50dB) or
> Blackman (-70dB) using firfilt(). See 'Tools' -> 'Filter the data' ->
> 'Windowed sinc FIR filter'.
>
> There are different guys saying different things about data preprocessing.
> It is confusing, I know! The only good solution for this is to become an
> engineer yourself...
>
> Makoto
>
>
>
> On Tue, Jan 24, 2017 at 7:00 AM, Ahmad, Jumana <jumana.ahmad at kcl.ac.uk>
> wrote:
>
>> Hi  Everyone,
>>
>> I am running a large scale ERP analysis. I filtered 1-40Hz (ICA AMICA),
>> or 0.1-40Hz for the ERP dataset. A 30Hz low pass does not help to get rid
>> of the oscillation, which is really significant in the data. I use a
>> butterworth filter, which is good for ERP analysis with low phase
>> distortion.
>>
>> I also already run ICA, but in some datasets there is a very significant
>> high frequency oscillation.
>>
>> I do not use cleanline, which is not typical in the literature I have
>> been basing my pipeline on.
>>
>>
>>
>> However, I can see the high frequency oscillations in my ERP, which is
>> not ideal and now I need to try and get rid of it further.
>>
>> Can I filter again on top of the data which already has already undergone
>> ICA- I only use ICA to remove blinks?
>>
>> Should I do cleanline, although it would have to be after ICA now- I read
>> this is not advisable.
>>
>> Should I use a notch filter?
>>
>>
>>
>> Any help would be appreciated.
>>
>> Best wishes,
>>
>> Jumana
>>
>>
>>
>> *------------------------------------------*
>>
>> *Jumana Ahmad*
>>
>> Post-Doctoral Research Worker in Cognitive Neuroscience
>>
>> *EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study*
>>
>> Room M1.09. Department of Forensic and Neurodevelopmental Sciences (PO
>> 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College
>> London | 16 De Crespigny Park | London SE5 8AF
>>
>>
>>
>> *Phone:* 0207848 0260| *Email:* jumana.ahmad at kcl.ac.uk
>> <antonia.sanjose at kcl.ac.uk> | *Website:* www.eu-aims.eu
>> <https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eu-aims.eu%2F&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C35190d19320946ffd52408d446355d20%7C8370cf1416f34c16b83c724071654356%7C0&sdata=vVSbBawKS2L6e9vVZXkIMrj%2B%2FwqhrreJRZRNr6zUN2s%3D&reserved=0>
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>>
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>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>

-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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