[Eeglablist] Question about Cleanline

[Tim Mullen]

Please also note that the authoritative reference on the methods underlying
Cleanline is not our PREP paper (which is an amalgam of third party tools).
The appropriate references and theory are provided in Cleanline's toolbox
documentation.

Tim
On Apr 6, 2016 3:34 AM, "Tim Mullen" <mullen.tim at gmail.com> wrote:

> Actually, that is not correct.
>
> Cleanline uses multitaper regression, with Thompson's F-statistic for
> determining the probability of sinusoidal artifact at a given frequency.
> There is no "Welch FFT" nor any need to high pass filter the data (this
> would have no effect on Welch's method either).
>
> Please see the documentation and references I have provided for Cleanline,
> in the toolbox Readme file on NITRC, paying attention to the "Tips on
> Running Cleanline" section:
> https://www.nitrc.org/projects/cleanline/
>
> Eric, you may try running Cleanline iteratively on the data, gradually
> increasing the significance threshold (LineAlpha). You may also try
> different window sizes, as suggested in the tips. Other tips there may also
> apply. If you have multiple epochs, ensure your window size and step size
> equal (or divide) the epoch length.
>
> You may also consult our PREP paper/toolbox, which wraps around Cleanline
> and local detrending tools I have previously discussed on this list, as
> well as other artifact rejection tools developed by Christian Kothe.
>
> Best,
> Tim Mullen
> On Apr 5, 2016 2:09 PM, "Makoto Miyakoshi" <mmiyakoshi at ucsd.edu> wrote:
>
>> 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.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
>>>
>>>
>>> [image: Inline image 1]
>>>
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>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
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