[Eeglablist] problem getting ICA to run properly on data files

Andreas Widmann widmann at uni-leipzig.de
Thu Apr 17 09:44:44 PDT 2014


Hi Emily,

I had a quick look at the ERPLAB filter code and I can see one potential problem. ERPLAB seems to expect the boundary events at .5-latencies between two samples (as produced by pop_mergeset). However, all raw file formats I’m aware of set the discontinuity/boundary triggers at integer latencies (first sample of new data segment). BVA-IO imports them unmodified. ERPLAB shifts the boundary events at integer latencies by one sample. This results in DC artifacts at segment/epoch ends for interrupted/paused recordings and a single unfiltered sample at the beginning of the dataset.

I would consider this as a potential bug in the ERPLAB filter as boundary events at integer latencies should not be shifted. I do not see a straightforward relation to the described problems with ICA. Are there potentially more „New Segment“ markers in the raw data (do you pause recording during breaks)?

Best,
Andreas

Am 17.04.2014 um 18:17 schrieb Emily Kappenman <eskappenman at ucdavis.edu>:

> Hi Andreas,
> 
> I think the issue had to do with the duration of the first event being recorded as 'NaN,' but I'm not entirely sure.  I've copied Javier Lopez-Calderon who programs/designs ERPLAB and might be able to more thoroughly describe the issue we encountered.  Javier, can you describe why this event code at the beginning of the Brain Products data files was causing issues with the ERPLAB filter?  
> 
> Thanks!
> -Emily
> 
> 
> On Thu, Apr 17, 2014 at 9:10 AM, Andreas Widmann <widmann at uni-leipzig.de> wrote:
> Hi Emily,
> 
> > Thanks for the response!  I think we have resolved this issue (or figured out a work around, at least).  For some reason I was getting a 'boundary' code at the beginning of my imported EEG files (using the File > Import data > Using EEGLAB functions and plugins > From Brain Vis. rec .vhdr file option), with a duration of 'NaN.‘
> The boundary event corresponds to the „New segment“ marker (correctly) set by default by BrainVision Recorder for the first sample of each segment (also the first one) of the recording. This event should not cause any problems for filtering. Also other recording software as e.g. Biosemi ActiView sets these markers (unfortunately the EEGLAB bdfimport plugin does not import them at all, even if the marker is not at the beginning of the file).
> 
> > This was causing errors in the filter I was using in ERPLAB related to aligning the sampling points, and this was causing ICA to not run properly.
> What kind of problem causes this in the ERPLAB filter? Could you please describe what you mean by „related to aligning the sampling points“?
> 
> Thanks,
> Andreas
> 
> > If I remove this code from the beginning of the data file, everything works normally again.  I'm not sure why this code was appearing (there are no event codes at that time point in the EEG data file, and we did not remove any segments in this time range offline either).  I'm also exploring other import methods, using the suggestions people have been providing in response to my other post.
> >
> > Please let me know if you have any additional suggestions.
> >
> > Thanks!
> > -Emily
> >
> >
> > On Wed, Apr 16, 2014 at 11:10 AM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu> wrote:
> > Dear Emily,
> >
> > I can think of multiple reasons, such as severe rank reduction, huge artifacts, continuous zeros, etc etc... to diagnose it I need to ask you to send me a sample data to reproduce the problem. Are you willing to do it?
> >
> > Makoto
> >
> >
> > 2014-04-09 16:17 GMT-07:00 Emily Kappenman <eskappenman at ucdavis.edu>:
> > Hi all,
> >
> > I have been using ICA for some time now to correct eye blink artifacts in EEG data files with lots of success, but I just started using a new EEG system and am running into problems getting ICA to run properly on the files.  I am encountering the following error message: error: runica(): QUITTING - weight matrix may not be invertible!
> >
> > This occurs on data files from multiple subjects, of different lengths, with different sampling rates, with different reference sites (both online and offline), etc..  Sometimes ICA will run but will require multiple separate components for eye blinks (5 or 6 out of 31 components).  The number of the components in the list that relate to the eye blinks also seems to correspond to channel numbers in a systematic way (e.g., if FP2 was channel 30 in the data set, component 30 is one of the components, etc.).
> >
> > Has anyone encountered anything like this before or have any ideas what might be causing this?  Any suggestions are much appreciated!
> >
> > Thanks so much!
> > -Emily Kappenman
> >
> > --
> > --------------------------------------------------------------------
> > Emily S. Kappenman, Ph.D.
> > UC Davis Center for Mind and Brain
> > 267 Cousteau Place
> > Davis, CA 95618
> > eskappenman at ucdavis.edu
> > --------------------------------------------------------------------
> >
> > _______________________________________________
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> >
> >
> > --
> > Makoto Miyakoshi
> > Swartz Center for Computational Neuroscience
> > Institute for Neural Computation, University of California San Diego
> >
> >
> >
> > --
> > --------------------------------------------------------------------
> > Emily S. Kappenman, Ph.D.
> > UC Davis Center for Mind and Brain
> > 267 Cousteau Place
> > Davis, CA 95618
> > eskappenman at ucdavis.edu
> > --------------------------------------------------------------------
> > _______________________________________________
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> 
> 
> 
> 
> -- 
> --------------------------------------------------------------------
> Emily S. Kappenman, Ph.D.
> UC Davis Center for Mind and Brain
> 267 Cousteau Place
> Davis, CA 95618
> eskappenman at ucdavis.edu
> --------------------------------------------------------------------



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