[FieldTrip] ft_redefinedata after pre-processing

Blume Christine christine.blume at sbg.ac.at
Mon Nov 26 18:30:47 CET 2018


Dear Silvia,

What you could do is do your downsampling, re-referencing, filtering and ICA on continuous data and save the resulting dataset as data1. Then, you do the artefact rejection on continuous data (unless you have long episodes that are of no interest, then you may reconsider) and save this to cfg_artifactrejection. That way, you obtain an artefact rejection file that is independent from epoching, sometimes not the worst idea. Then you go back and load data1, do the epoching, and then do the artefact rejection.

Best,
Christine


Von: fieldtrip <fieldtrip-bounces at science.ru.nl> Im Auftrag von Silvia Formica
Gesendet: Montag, 26. November 2018 16:12
An: FieldTrip discussion list <fieldtrip at science.ru.nl>
Betreff: Re: [FieldTrip] ft_redefinedata after pre-processing


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!

Silvia

________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Blume Christine <christine.blume at sbg.ac.at<mailto:christine.blume at sbg.ac.at>>
Sent: 26 November 2018 15:43
To: fieldtrip at science.ru.nl<mailto: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=[];
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…

Best,
Christine

Von: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> Im Auftrag von Silvia Formica
Gesendet: Montag, 26. November 2018 14:19
An: fieldtrip at science.ru.nl<mailto: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=[];

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!



Best,

Silvia




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