[FieldTrip] sliding window for ICA

[Russell G Port]

Thank you Dr Schurger, this is awesome


On Sat, Feb 22, 2014 at 10:37 AM, Aaron Schurger
<aaron.schurger at gmail.com>wrote:

> See below...
>
>
> On Sat, Feb 22, 2014 at 12:27 AM, Russell G Port <russgport at gmail.com>
> wrote:
> > Hi All,
> >
> > I have come across a problem and was hoping that someone had
> experience/knew
> > things that could be useful.I have some MEG data, and the effort
> currently
> > is to remove noise and artifact. I have the line noise reduction working
> > fine, the question that faces me is the following. When I first read in
> my
> > data I have the option of one of two methods. I can read it in as 1
> second
> > epoch for the whole length of the experiment (contiguous time bins, with
> no
> > regard to events), or create 1 second epochs centered around a certain
> > trigger (the data contains 4 different triggers). Initially I wanted to
> read
> > in 1 second epochs (that spanned the entire dataset), clean it of
> artifacts
> > (jumps, muscle, EOG,ECG, anything else), which would remove bad trials
> and
> > components. I had then hoped to redefined the epoch, so that I could
> create
> > 4 separate subsets of data, each centered around a separate trigger. It
> > appears that I cannot do this (fieldtrip actually refuses this
> > specifically). Is this because of issues with phase/jitter when putting
> the
> > samples back together in different time sets? Second, it has been
> suggested
> > that we perform ICA analysis to detect EOG and ECG artifacts on the data
> > parsed just by timing (i.e. 1second bins contiguous for the entire
> length of
> > the data but no relation to triggers), and have the component rejection
> scan
> > my trials that are actually binned the based on triggers to remove the
> > components; even though this is not the exact epochs used to classify the
> > components. Is this possible?
>
> This is the preferred way to do it. Read in all of your data in 1- or
> 2-second epochs at arbitrary points (just one right after another).
> Run ICA on these epochs and save the components that you get (call
> this 'comp'). Then make a note of the components that you want to
> remove (usually blink, eye movement, and heart). Now read in your data
> time-locked to your triggers and use the previously-defined components
> to clean up the data (use the cfg to specify which components you want
> to remove).
> [data] = ft_rejectcomponent(cfg, comp, data);
>
> >
> > While I think it would be better to do the artifact correction on the
> whole
> > dataset (all time/triggers included), would it actually be better to
> first
> > define trials by triggers and then repeat everything (artifact
> > rejection-wise)? This is very easy to do (and I have), the only issue
> comes
> > when trying to compare the using ft_timelockanalysis/ft_freqanalysis (as
> in
> >
> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_ecg_artifacts?s[]=ecg
> ).
> > I have the issue that when I used ft_artifact_ecg to detect peaks in the
> ECG
> > channel (via z scores), zeros and NaNs are returned, and it fails to
> graph;
> > since often the ECG timing occurs with such timing that the full pre/post
> > time extends past what is actually in the trial. Is it proper just to
> remove
> > all ECG events that cross the boundaries of the trigger based trials from
> > the trial definitions  used in next step. Here the sections of data
> > contaminated with ECG are parsed and then tested to see coherence to the
> ICA
> > components? I would fear that this would produce erroneous results, since
> > the data for the ica would include the partial ECG event that I threw
> out.
> >
> > Best
> > Russ Port
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Aaron Schurger, PhD
> Senior researcher
> Laboratory of Cognitive Neuroscience
> Brain-Mind Institute, Department of Life Sciences
> École Polytechnique Fédérale de Lausanne
> Station 19, AI 2101
> 1015 Lausanne, Switzerland
> +41 21 693 1771
> aaron.schurger at epfl.ch
> http://lnco.epfl.ch/
>
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