[FieldTrip] Automatized artifact rejection in FT

[Herring, J.D. (Jim)]

Hi Ricarda,

I’m not sure if that is what you want but you could see whether a time-shifted version of your data (+200ms) differs more than 3uV from your original data. To shift your data you can use ft_redefinetrial with cfg.offset = -samples, where samples is the amount of samples from the original zero-point you wish to shift your time series by. Subtracting those time-series should give you the difference between t and t+200ms.

Best,

Jim

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Ricarda Braukmann
Sent: woensdag 18 november 2015 14:42
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Automatized artifact rejection in FT

Hi Jim,
Thanks for the quick reply, this is really helpful.
I will try your suggestion for number three.

Regarding the second criteria, we indeed want to exclude changes of more than 3uV between t and t+200ms.
So if you have any suggestion of how we might be able to implement this as well, that would be great!
Thanks!
Ricarda

On Wed, Nov 18, 2015 at 2:14 PM, Herring, J.D. (Jim) <j.herring at donders.ru.nl<mailto:j.herring at donders.ru.nl>> wrote:
Hi Ricarda,

All three criteria have a certain threshold that has to be met in order for a trial to be marked as containing artifacts so for all criteria you could use ft_artifact_threshold (or ft_artifact_zvalue). The difference will be how you preprocess the signal. You would need to transform the signal so that for criteria nr. 2 the signal represents the potential difference over a 200ms window?, and for nr. 3 the potential difference per sampling point.

Number 3 is relatively easy, you can calculate the first temporal derivative (ie. the difference between two consecutive samples) with cfg.artfctdef.threshold.derivative = ‘yes’ (or ….threshold.absdiff = ‘yes’, if you want the absolute difference). So something like this should work:

cfg.artfctdef.threshold.channel   = cell-array with channel labels
cfg.artfctdef.threshold.bpfilter  = 'no';
cfg.artfctdef.threshold.absdiff = ‘yes’;
cfg.artfctdef.threshold.max       = 50;

Number 2 is slightly more difficult because you want to integrate over a larger window. I don’t fully understand what you want to avoid, should the signal at time X stay within 3uV of the signal at time X + 200ms?

Best,

Jim



From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [mailto:fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] On Behalf Of Ricarda Braukmann
Sent: woensdag 18 november 2015 12:58
To: FieldTrip discussion list
Subject: [FieldTrip] Automatized artifact rejection in FT

Hi everyone,
I would like to implement an automatized artifact rejection procedure for my EEG data and compare this to manual rejection.

I would like to use the following criteria for rejection of a segment:

1. amplitudes below -150 or above 150 µV
2. a difference of 3 µV per 200 ms,
3. or a voltage change of 50 µV per sampling point
Is there a function in fieldtrip that I can use for implementing these different criteria?
I know that FT_ARTIFACT_THRESHOLD can reject segments on basis of the first criteria but I am unsure how to implement the second two.
Any help would be highly appreciated.
Thanks!
Ricarda


--

Ricarda Braukmann, MSc
PhD student

Radboud University Medical Centre & Baby Research Center

Donders Institute for Brain, Cognition and Behaviour,
Centre for Neuroscience & Centre for Cognition

Room B.01.22
Phone: +31 (0) 24 36 12652
Email: r.braukmann at donders.ru.nl<mailto:r.braukmann at donders.ru.nl>
Website: http://www.zebra-project.nl/



--

Ricarda Braukmann, MSc
PhD student

Radboud University Medical Centre & Baby Research Center

Donders Institute for Brain, Cognition and Behaviour,
Centre for Neuroscience & Centre for Cognition

Room B.01.22
Phone: +31 (0) 24 36 12652
Email: r.braukmann at donders.ru.nl<mailto:r.braukmann at donders.ru.nl>
Website: http://www.zebra-project.nl/
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