[FieldTrip] Amplifier for EGI-data in fieldtrip???

Joseph Dien jdien07 at mac.com
Fri Sep 7 03:07:12 CEST 2012


I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed.  I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in).  I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values.  So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file.  My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI.

Joe


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On Sep 6, 2012, at 1:01 PM, Matt Mollison <matt.mollison at gmail.com> wrote:

> Joe,
> 
> A few related questions:
> 
> Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation?
> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages.
> 
> Thanks,
> Matt
> 
> --
> Univ. of Colorado at Boulder
> Dept. of Psychology and Neuroscience
> matthew.mollison at colorado.edu
> http://psych.colorado.edu/~mollison/
> 
> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien <jdien07 at mac.com> wrote:
> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them).  I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files.  It's a bit disconcerting to say the least.  I could take a look at your files if you'd like confirmation.
> 
> Joe
> 
> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis <inieuwenhuis at BERKELEY.EDU> wrote:
> 
>> Hi Daria,
>> 
>> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find.
>> 
>> Cheers,
>> Ingrid
>> 
>> 
>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote:
>>> Hi Daria,
>>> 
>>> There might indeed be an incompatibility in the gain  value applied to the data.
>>> 
>>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats.
>>> 
>>> best regards
>>> Robert
>>> 
>>> 
>>> 
>>> 
>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote:
>>> 
>>>> Dear Fieldtrippers,
>>>> 
>>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. 
>>>> The ERPs look perfect. 
>>>> The 'only' problem is, that my signals look to strong.
>>>> It looks like if I get amplitutes (average) until 70 ┬ÁV. 
>>>> I think it must be an intern amplifier for the signals.
>>>> Does anyone know this problem with EGI-data?
>>>> 
>>>> Or does anyone know, where I can see the amplifier?
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Greetings,
>>>> 
>>>> Daria _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> -- 
>> Ingrid Nieuwenhuis PhD
>> Postdoctoral Fellow
>> Sleep and Neuroimaging Laboratory
>> Department of Psychology
>> University of California, Berkeley
>> California 94720-1650
>> Tolman Hall, room 5305
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> --------------------------------------------------------------------------------
> 
> Joseph Dien,
> Senior Research Scientist
> University of Maryland 
> 
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://joedien.com//
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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--------------------------------------------------------------------------------

Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdien07 at mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//










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