[Eeglablist] Inconsistent results using clean_artifacts

Tue Mar 8 10:36:41 PST 2022

Dear Cristina,

Glad that you resolved it.

In this paper
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.frontiersin.org_articles_10.3389_fninf.2015.00016_full&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=6anBLYbp7QdHJFldL-5RHDUW8DOQDjVahfBeCIwkWRS7uwprMh8nahAmV7-npm_k&s=8bjRx5pTnD7zN6J5arUoUdyoWrU2e6a9vavVoWblXOc&e= >(PREP
pipeline), you might find the reasons why RANSAC was proposed. For a better
estimation using RANSAC, you might use a higher value for the variable
num_samples (which is 50, by default).

If you have larger datasets, these differences shouldn't be a problem. My
suggestion would be to follow Makoto's alternate solution (to disable
clean_rawdata for channel removal and to use the simplest measures).

Best regards,

Velu Prabhakar Kumaravel, Ph.D. Student
Center for Mind/Brain Sciences,
University of Trento, Italy

On Tue, 8 Mar 2022 at 17:58, Gil Avila, Cristina via eeglablist <
eeglablist at sccn.ucsd.edu> wrote:

> Dear Prabhakar and Makoto,
>
> Thank you for your responses. I have tried both
> 1) Uncomment the lines in clean_channels() that fix the seed for random
> stream and
> 2) Keep the clean_channels() code as it as and fix in my code the seed of
> the random number generator: rng('default');
>
> In both cases I get a stable set of bad channels although the set of bad
> channels in 1) is different than the set of bad channels in 2). These
> 'tricks' make stable the bad channel detection. Nevertheless, I am
> concerned about the RANSAC algorithm itself. I believe it is suboptimal
> that, depending on how the channels were initially chosen,  different sets
> of bad channels are given as an output. I don't know if this will have an
> impact on later results such as power effects between groups. Do you think
> that this channel discrepancy will impact later results or do you think
> that it will be diluted when looking into large datasets?
>
> Best,
> Cristina
>
> -----Original Message-----
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> Sent: Thursday, 3 March 2022 18:40
> To: eeglablist at sccn.ucsd.edu
> Subject: Re: [Eeglablist] Inconsistent results using clean_artifacts
>
> Dear Cristina,
>
> Sorry for the inconvenience.
>
> > I am using the last version of clean_rawdata plugin and every time
> > that I
> run clean_rawdata on the same dataset I get a different set of 'bad
> channels'. Is this problem fixed?
>
> According to this page, clean_channels() was updated 2 years ago. Without
> testing, I guess it is probably not fixed.
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sccn_clean-5Frawdata&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=8vkQdVejMdf_IHSTIf0e5McIIPD3TbqIxIXVpdRjCZxECTENaMdkB4EoFHSDinQX&s=yz8W2rwlcw_xyQhxNND6QqqHF0ahjP6l7vk_BsP5sgw&e=
>
> If I remember correctly, it uses RANSAC which uses 'repeated random
> subsampling'. The unstable output is a nature of the algorithm and it
> cannot be 'fixed'.
> I know this is an annoying issue. We always prefer to use deterministic
> approaches for the purpose of reproducibility.
>
> Here are my suggested work arounds.
> 1. This is a little bit technical, but you can fix the seed of a random
> number generator by using rng(). Theoretically, this guarantees the
> complete reproducibility from the algorithm. In clean_channels() line 171,
> you can see the following line commented out. I don't know why it is
> commented out, but if you can fix the seed for the random number generator
> there, it may work out. I would try rng() instead of what is there now.
> %stream = RandStream('mt19937ar','Seed',435656);
>
> 2. Alternatively, you disable the electrode removal function in
> clean_rawdata() and perform your own electrode rejection process.
> Sometimes even a simple max value approach like the one used in
> trimOutlier() is sufficient, so you may try it out.
>
> Makoto
>
>
> On Wed, Mar 2, 2022 at 9:01 AM Gil Avila, Cristina via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
> > I would like to reopen a topic from 2020 regarding the consistency of
> > clean_artifacts. I am using the last version of clean_rawdata plugin
> > and every time that I run clean_rawdata on the same dataset I get a
> > different set of 'bad channels'. Is this problem fixed? Specifically I
> am running:
> >
> > EEG =
> > pop_clean_rawdata(EEG,'FlatlineCriterion',5,'ChannelCriterion',0.8,'Li
> > neNoiseCriterion',4,'Highpass',[0.25
> > 0.75],'BurstCriterion','off','WindowCriterion','off','BurstRejection',
> > 'off','Distance','Euclidian','WindowCriterionTolerances','off');
> >
> > Best,
> > Cristina Gil
> > --
> > Cristina Gil Ávila - PhD candidate
> > Department of Neurology
> > Technische Universität München
> > Munich, Germany
> > cristina.gil at tum.de<mailto:cristina.gil at tum.de>
> > painlabmunich.de<
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.painlabmunich
> > .de_&d=DwIFAw&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm
> > 1p6x6e36h3EglE&m=c_kRevMMCP43N5DUC96kTPQlI81ezyGf6D0jCBCbtNsjpI0SNRrFx
> > tNyOi0J1P05&s=nZ9fhNHv4Zt2tPe1W18k_LDsgbW7YJcgl9PBRpNInAk&e=
> > >
> >
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