[Eeglablist] Inconsistent results using clean_artifacts

[Makoto Miyakoshi]

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,'LineNoiseCriterion',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=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=c_kRevMMCP43N5DUC96kTPQlI81ezyGf6D0jCBCbtNsjpI0SNRrFxtNyOi0J1P05&s=nZ9fhNHv4Zt2tPe1W18k_LDsgbW7YJcgl9PBRpNInAk&e=
> >
>
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