[FieldTrip] Question re: TMS-EEG FT Tutorial

[Bingshuo Li]

Hi Jim,

Thank you very much again for your thoughtful response! I truly appreciate
it! I see your point now why you interpolate after ICA. It makes sense and
I think your argument is very valid. Indeed, bad channels always come up
fairly independently anyways. I can for sure do my channel inspection after
the ICA.

Another question along the same line: Would you suggest to categorize all
the IC with more than, say 30 uV, on the time-locked averaged IC, as muscle
artifacts as suggested by Korhonen et al. (2011)? I often feel very puzzled
when it comes to picking up ICs for removal. I feel that if I remove those
high amplitude ICs, my averaged TEPs look worse. However, by keeping those
high amplitude ICs, I am letting in signals with no biological
plausibility. Any thoughts on that?

Thanks very much!

Regards,

Bingshuo

-----
Bingshuo Li (MSc. candidate)
Systems Neurophysiology Group
Centre for Integrative Neuroscience
University of Tuebingen
Otfried-Mueller-Str. 25
D-72076 Tuebingen, Germany
bingshuo.li at student.uni-tuebingen.de
+49-7071-29-89029


On Fri, Apr 11, 2014 at 12:48 PM, Herring, J.D. (Jim) <
j.herring at fcdonders.ru.nl> wrote:

> Dear Bingshuo,
>
>
>
> I am forwarding your e-mail to the Fieldtrip mailinglist so that others
> can benefit and/or contribute from our discussion.
>
>
>
> The reason why I like to postpone the interpolation to after the ICA is
> that I noticed that when interpolating before ICA the interpolated data
> would load onto one component. Removing this component did not make sense
> as it would leave a flat line in the TEP, keeping it in did not make sense
> either because the interpolation was done with, for example, the decay
> artifact still in the data. After removing the decay artifact with ICA you
> would be left with a sharp peak in the interpolated segment.
>
>
>
> I see that it is difficult to reject trials and channels before
> interpolation but keep in mind that before having done ICA large amounts of
> variance of the data can be explained by the TMS related artifacts, these
> will most likely cloud the detection of other types of artifacts with
> functions such as ft_rejectvisual.
>
>
>
> In my experience bad channels show up as separate independent components
> anyway and can be removed after having run the ICA, but that may depend on
> a number of factors I’m not aware of.
>
>
>
> If you would like to reject bad channels prior to running ICA you could
> also try to run ft_rejectvisual and specify cfg.latency to contain only
> your pre-TMS period or a period post-TMS that does not contain any large
> artifacts. That way you should at least be able to run metrics on your data
> to remove bad channels. In any case you can always run ft_databrowser on
> your data to visually inspect your channel time courses for bad channels
> prior to running the ICA.
>
>
>
> In any case you are of course free to try running the ICA after
> interpolation yourself and share your experiences, perhaps this works fine
> for you J
>
>
>
> Best,
>
>
>
> Jim
>
>
>
> *From:* Bingshuo Li [mailto:bingshuo.li at cin.uni-tuebingen.de]
> *Sent:* donderdag 10 april 2014 16:36
> *To:* j.herring at fcdonders.ru.nl
> *Subject:* Question re: TMS-EEG FT Tutorial
>
>
>
> Dear Jim,
>
> I inquired you about a TMS-EEG question a while ago and you referred me to
> the TMS-EEG tutorial on Fieldtrip's website. As I was following the steps
> of the tutorial, there is a new question that come up to me -- Is it really
> necessary to postpone the interpolation of the TMS artifact until the ICA
> is done? Would there be any bad consequences if I interpolate first and
> then run the ICA over the entire interpolated trial(s)? The reason I am
> asking this question is that I would like to visually inspect my data first
> and remove bad channels or trials (if any) prior to ICA. If the artifact is
> not interpolated, it is really difficult to run visual inspection or
> metrics on the data.. Following the logic of the tutorial, I can only
> visual inspection after the ICA, which I think might not be a good idea as
> I was told that a bad channel can easily bias the ICA result..
>
> Do you have any insights in this? Thank you very much for your time in
> advance!
>
> Sincerely,
>
>
> -----
> Bingshuo Li (MSc. candidate)
> Systems Neurophysiology Group
> Centre for Integrative Neuroscience
> University of Tuebingen
> Otfried-Mueller-Str. 25
> D-72076 Tuebingen, Germany
>
> bingshuo.li at cin.uni-tuebingen.de
>
> +49-7071-29-89029
>
>
>
> On Mon, Feb 10, 2014 at 3:24 PM, Herring, J.D. (Jim) <
> j.herring at fcdonders.ru.nl> wrote:
>
> Dear Bingshuo,
>
>
>
> Please have a look at the following tutorial:
> http://fieldtrip.fcdonders.nl/tutorial/tms-eeg
>
>
>
> It deals with a number of TMS-EEG related artifacts including the ‘evil’
> decay artifact.
>
>
>
> Best,
>
>
>
> Jim
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Bingshuo Li
> *Sent:* maandag 10 februari 2014 15:06
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] TMS-EEG Decay Artifact
>
>
>
> Dear FT users and developers,
>
> Does anyone have any experience in dealing with the so-called decay
> artifacts found in TMS-EEG? It is a relatively long lasting (up to 100ms)
> artifact that follows a waveform similar to exponential decay and it occurs
> sporadically in certain recording channels.
>
> Any tips/hints/recommendations are greatly appreciated! Thank you!
>
> Regards,
>
>
>
> -----
> Bingshuo Li (MSc. candidate)
> Systems Neurophysiology Group
> Centre for Integrative Neuroscience
> University of Tuebingen
> Otfried-Mueller-Str. 25
> D-72076 Tuebingen, Germany
> bingshuo.li at student.uni-tuebingen.de
> +49-152-06054831
>
>
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