[FieldTrip] Dealing with warning message "data contians NaN values"

[Stephen Whitmarsh]

Dear Jeremy,

Welcome to the FieldTrip community!

Could you be more specific about "the data looks incorrect in the end.",
and perhaps share a screenshot if informative? Sharing the relevant part of
your script would be helpful too. For more info about how to get the best
response to your questions, please take a look at:
http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community/

Have you checked where the NaN's in the data are, and whether they appear
before or after downsampling?

Just an shot in the dark, but have you perhaps defined your trials for
epoching (i.e. the samples in the .trl) based on the old samplerate?

Cheers,
Stephen





On Thu, 18 Jul 2019 at 12:35, Jeremy Pulmano <jpulmano at princeton.edu> wrote:

> Hi,
>
> I've realized that the warning message often comes right after epoching
> (using ft_definetrial and then ft_redefinetrial). It seems like it
> successfully breaks the data into segments but still contains NaNs for
> whatever reason. Here are more details about the pipeline so far:
>
>    1. High pass filtering (0.1 Hz / FIR / order = 100)
>    2. Downsampling (1024 to 128 Hz)
>    3. Epoching (prestim 0.1, poststim 0.4)
>    4. Base-line correction [ -0.1 0 ]
>    5. Re-referencing (common avg.)
>    6. ICA / component rejection
>    7. Visual artifact removal
>    8. Low pass filter (30 Hz)
>
> Any further help would be greatly appreciated.
>
> Thanks,
> Jeremy
>
> On Wed, Jul 17, 2019 at 4:57 PM Jeremy Pulmano <jpulmano at princeton.edu>
> wrote:
>
>> Hi Erika,
>>
>> The original sampling rate is 1024 Hz and the new sampling rate is 128 Hz.
>>
>> Thanks,
>> J
>>
>> On Wed, Jul 17, 2019 at 4:49 PM Erika Puiutta <
>> erika.puiutta at uni-oldenburg.de> wrote:
>>
>>> Hey J,
>>>
>>> this is just an educated guess since I don't really know how fieldtrip
>>> does the downsampling, but what is your sampling frequency and the sampling
>>> frequency you sample down to? Is it possible that your downsampling
>>> frequency is not a harmonic of your original sampling frequency (say 1000Hz
>>> to 300Hz)? Maybe there are NaNs for the new samples where fieldtrip can't
>>> find a corresponding one from the old sampling frequency?
>>>
>>> Best of luck,
>>> Erika
>>>
>>> Am 17.07.2019 um 17:26 schrieb Jeremy Pulmano <jpulmano at princeton.edu>:
>>>
>>> Hi all,
>>>
>>> I am new to both neuroscience and FieldTrip and am trying to debug my
>>> preprocessing pipeline of EEG data (biosemi .bdf files). These are the
>>> current steps:
>>>
>>>    1. High pass filtering
>>>    2. Downsampling
>>>    3. Epoching
>>>    4. Base-line correction
>>>    5. Re-referencing
>>>    6. ICA / component rejection
>>>    7. Visual artifact removal
>>>    8. Low pass filter (I save the low pass filter for the end so that
>>>    ICA yields better time course plots).
>>>
>>> However, after the first three steps (high pass, downsample, epoch), I
>>> continue to get the warning message: "Warning: data contains NaN values, no
>>> filtering or preprocessing applied," starting at baseline correction. It
>>> repeats itself over and over again. If I ignore these errors, the data
>>> looks incorrect in the end. Why does this happen, and how can I resolve
>>> this?
>>>
>>> Any tips would be appreciated.
>>>
>>> Thanks,
>>> J
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>> --
>>
>> *Jeremy Pulmano*
>> *Princeton University Class of 2021*
>> B.S.E. Computer Science
>> e: jpulmano at princeton.edu | c: (862) 220-5903
>>
> _______________________________________________
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> https://doi.org/10.1371/journal.pcbi.1002202
>
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