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

Matt Mollison matt.mollison at gmail.com
Thu Sep 13 16:50:58 CEST 2012


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//
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>> 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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