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

Daria Laptinskaya daria.laptinskaya at googlemail.com
Thu Sep 13 17:14:37 CEST 2012


There is a formula in the NetStation-manual: (5000 mircovolts / (2^16 bits).
You can convert bits to microvolts by multiplicating all signals with the
factor 0,076293945 in fieldtrip.
This solution isn't perfect, because it doesn't consider gains.
We asked EGI for an other formula, but didn't yet get an answer.
I compare the two methods and for little N the gains don't make a great
difference.


Best,
Daria





2012/9/13 Matt Mollison <matt.mollison at gmail.com>

> Daria,
>
> I do not know any calibration function for raw files that were exported
> without calibration, but maybe it is a simple formula? You might want to
> contact EGI. Let us know if you find anything out.
>
> Best,
> Matt
>
> --
> Univ. of Colorado at Boulder
> Dept. of Psychology and Neuroscience
> matthew.mollison at colorado.edu
> http://psych.colorado.edu/~mollison/
>
> On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya <
> daria.laptinskaya at googlemail.com> wrote:
>
>> Yes, it works fine now-thank you!!!
>>
>> @Matt: Do you know a calibration-function for existing raw-files?
>>
>>
>>
>> Best,
>>
>> Daria
>>
>>
>> 2012/9/10 Joseph Dien <jdien07 at mac.com>
>>
>>> Hey Daria,
>>>    glad you were able to get it worked out!  Thank Matt for his reminder
>>> (below) about the calibration option.
>>>
>>> Cheers!
>>>
>>> Joe
>>>
>>>
>>> Hi Joe,
>>>
>>>
>>> I didn’t know that there is a function like this.
>>>
>>> The most of my colleagues use the RAW.-files they get from the
>>> file-exporter without problems.
>>>
>>> Not even NetStation-support could give me an answer.
>>>
>>> So I thought, it must be a problem between NetStation and fieldtrip.
>>>
>>> Because of your tip I opened an original datafile and tried to save a
>>> copy of the file.
>>>
>>> Doing so NetStation offers a possibility to ‘convert to microvolts’ and
>>> create a .ses –datafile.
>>>
>>> The .raw-files I get this way have microvolt as unit.
>>>
>>> I compared the signals I get this way with the signals I get by using
>>> the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the
>>> same-that’s great!!!
>>>
>>> It seems to work now.
>>>
>>> Thank you very much!!! You were a great help!!!
>>>
>>>
>>> Cheers,
>>>
>>> Daria
>>>
>>> On Sep 6, 2012, at 9:07 PM, Joseph Dien <jdien07 at mac.com> wrote:
>>>
>>> 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
>>>
>>>
>>>
>>> --------------------------------------------------------------------------------
>>>
>>> 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
>>>
>>> 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 µV.
>>>> 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 listfieldtrip at donders.ru.nlhttp://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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>>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
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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//
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --------------------------------------------------------------------------------
>>>
>>> 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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>
>
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