[Eeglablist] DC shifts in biosemi files: first do a baseline correction and then a high pass filter

Jake Anderson ande2523 at umn.edu
Mon May 24 10:34:50 PDT 2010


Or... you could just start recording the data file 10-20 seconds before the 
first important event and stop recording 10-20 seconds after the last 
important event, and you'd almost always avoid having any filter artifacts 
anywhere near critical data points. Freshly collected, raw .bdf data is 
continuous, right? So what exactly are you baseline correcting?

*************************************************
Jacob E. Anderson, MA
Junior Scientist
Zelazo Lab
Institute of Child Development
University of Minnesota




On May 22 2010, seba wrote:

>Dear all,
>
> as many of you know and have discussed on this list before (see for 
> example post by Brad, september 12th, 2008),
> Biosemi .bdf files look very weird when you open them for the first time 
> in Matlab (with or without Eeglab).
> In fact the amplitudes are completely shifted and out of range ("because 
> BioSemi uses some of its bit depth to record the DC offsets", as Brad 
> says).
> And the solution for this problem was said to be simple: just apply a 
> high-pass filter (e.g. at 0.1 Hz) and everything gets back into the 
> normal range again.
>
> However, as I found out, if you do so for example with a butterworth 
> filter, you get a huge artifact which forces you to throw away parts of 
> your data in the beginning.
> Actually, when the amplitude shift is huge, and even more so if I use a 
> filter with a high order, it looks like the ENTIRE EEG (!!?) is polluted 
> by this artificially introduced artifact.
>
> Thus, I would like to remind all people working with Biosemi files to 
> FIRST do a baseline correction, and only then, apply their filters.
>Doing so does not (at least on my data) result in this filter artifact.
>
> Just so that you see it yourself, you can try this little script in 
> Matlab,
> in which I just construct and then shift an artificial signal, and where 
> the signal becomes really ugly after filtering:
>
>
>%%%%%%%%%%%%%%%
>clear all
>clc
>
>x=-10*pi:0.001:10*pi;
>y=sin(x)+1000000; %introduce an amplitude shift
>
>%%filter with a 5th order butter. In this case I the sampling frequency is
>%%defined as 1024
>[z,p,k] = butter(10, .1/(1024/2), 'high'); 
>[sos, g] = zp2sos(z,p,k);
>h1 = dfilt.df2sos(sos,g);
>hfvt = fvtool(h1, 'FrequencyScale', 'log'); %plot
>eeg_filt = filter(h1, y(:,:)); %apply the filter
>
>%plot the 
>figure; subplot(2,1,1);
>plot(y(1:end));
>subplot(2,1,2);
>plot(eeg_filt(1:end));
>
>
>
>Sebastian Korb, Ph.D. Student
>Swiss Center for Affective Sciences
>University of Geneva, Switzerland
>Tel.: +41223799812
>Email: Sebastian.Korb at unige.ch
>http://www.affective-sciences.org/user/34




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