[FieldTrip] ft_redefinedata after pre-processing

Silvia Formica Silvia.Formica at UGent.be
Mon Nov 26 16:11:48 CET 2018

Dear Christine,

thank you for your quick response!

In my example data_cue is epoched and pre-processed.

Nevertheless, I think the approach you suggested might work also in my case. I also downsample, re-reference and filter the continuous data. After these first steps, I epoch the cue-locked dataset. After epoching, I perform artifact rejection and ICA.

I guess I can apply your approach to my data by running this exact same pipeline and saving the "cfg_artifactrejection" and my ICA components. Then I would go back to the filtered continuous data, epoch them target-locked and apply to this target-locked dataset the "cfg_artifactrejection"? saved before and removing the same ICA components selected before.

Do you think this would be an acceptable approach?

Thanks a lot!


From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Blume Christine <christine.blume at sbg.ac.at>
Sent: 26 November 2018 15:43
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] ft_redefinedata after pre-processing

Dear Silvia,

Do I understand correctly that data_cue is epoched, but not pre-processed?

You can apply ft_rejectartifact after ft_redefinetrial. We usually pre-process continuous datasets and save the cfg of this pre-processing (in the example below cfg_myartifactrejection). Only then we epoch the data and apply this artifactrejection.

cfg.trl=trl;                            # trl contains the trial definition of target-locked epochs

data_target = ft_redefinetrial (cfg, data_cue)

cfg = [];
data_target_clean = ft_rejectartifact(cfg_myartifactrejection, data_target);

I hope this helps...


Von: fieldtrip <fieldtrip-bounces at science.ru.nl> Im Auftrag von Silvia Formica
Gesendet: Montag, 26. November 2018 14:19
An: fieldtrip at science.ru.nl
Betreff: [FieldTrip] ft_redefinedata after pre-processing

?Dear all,

I'm in need of suggestions on the correct analyses strategy for my data.

I have an experiment with a cue followed (after ~2 seconds) by a target.

I epoched the data cue-locked and pre-processed my dataset. In my preprocessing I'm downsampling, re-referencing, rejecting some trials, running ICA, etc etc.

My problem is that I would want to also epoch my data target-locked, but I want to do it after pre-processing the cue-locked dataset. This is because I want to exclude the same trials and apply exactly the same corrections to the two different datasets.

I tried to use the function ft_redefinetrial, creating the new probe-locked trial definition and applying it to the cue-locked dataset.


cfg.trl=trl;                            # trl contains the trial definition of target-locked epochs

data_target = ft_redefinetrial (cfg, data_cue)

But I do not obtain what I wished for, because I get a data_target dataset that doesn't account for the trial rejection I performed while pre-processing the cue-locked dataset.

So my questions are:

1) is it possible to achieve my goal?

2) If yes, what is the right strategy to do it?

Thanks for any input and suggestion!



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