[FieldTrip] Question re: TMS-EEG FT Tutorial

[Herring, J.D. (Jim)]

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 <tel:%2B49-152-06054831> 


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20140411/9e38cc89/attachment.html>