[Mne_analysis] trouble reading the triggers in a .BDF file

[David Soto]

Hi Teon,

thanks for pointing me to the mask argument, I´ve just tried it and the
integer values and their numbers are not yet closer to what is expected,
however.  To be exact the trigger values that were sent to the biosemi were
between 0 and 36 (rather than 0- 32 as noted in my prior email, apologies
for that)
and there could be also 64 trigger values (if there were response errors on
some trials).

I am not too sure  the mask parameter as given  ' mask=2**17 - 32 ' has to
be changed as 0- 64  is also represented in the first  6 bites, but I may
be missing something.  What is the 32 in  ' mask=2**17 - 32 ' representing?

thanks again,
david

On 5 June 2016 at 19:28, Teon Brooks <teon.brooks at gmail.com> wrote:

> Hi David,
>
> The BDF file does have the original stimulus channel.
>
> Since your trigger values are represented from 0 to 32 (first six bits)
> and we permit trigger values up to 2**17 (some DIO triggering device can
> permit up 24bit triggers), you will need to mask the higher bit values of
> the trigger channel.
>
> This can be done with the function, mne.find_events(raw=raw, mask=2**17 -
> 32). This should provide you with your triggers.
>
> I just started a discussion
> <https://github.com/mne-tools/mne-python/issues/3284> on github about
> this mask argument, and there might be an API change to make it more
> user-friendly. As for now, this would be the solution to your problem.
>
> HTH
>
>
> teon
> --
> Teon Brooks <http://teonbrooks.github.io>, PhD Candidate
> twitter: @teon_io <http://www.twitter.com/teon_io>
>
> On Sun, Jun 5, 2016 at 4:45 AM, David Soto <d.soto.b at gmail.com> wrote:
>
>> Hi Teon,
>>
>> thanks for the message. True I uploaded .edf version of the original .bdf
>> the original pdf can be found here
>> https://drive.google.com/open?id=0B0PbSnFq24yMZWxoWGNFNGctQmM
>> I think the channel info was 'STI 014' as this appears to be the only
>> place where I get events id
>>
>> [ 65281  65282 etc]
>>
>>
>> definitely I am missing something in how to read the triggers from biosemi
>>
>> Looking at mne.io.read_raw_edf, there appears to be required an
>> annotation file and annotation map to interprete the stim_channel...but am
>> not clear what is to be done here
>>
>>
>> cheers,
>> david
>>
>> On 5 June 2016 at 03:13, Teon Brooks <teon.brooks at gmail.com> wrote:
>>
>>> Hi David,
>>>
>>> I just had a look at your edf file that you uploaded, and quick
>>> question, is this the correct file or is there a .BDF that you are trying
>>> to analyze?
>>> I had a look at the header of this file, and there isn't a stim channel
>>> listed ($head Anna\ Priming-edf.edf). Here, I see that there are 132 EEG
>>> channels, and two reference channels. Is this the same file your colleague
>>> looked at, if so, what channel did they see the corresponding trigger
>>> channels on?
>>>
>>> Quick explanation for what you saw on the supposed trigger channel: the
>>> reader assumes the last channel of the data block is the stimulus channel
>>> (i.e. stim_channel=-1), which is the typical setting. The values you saw
>>> were the software attempt to decode the stim channel values.
>>>
>>> You can look to see how the test data for edf and bdf list either
>>> triggers or annotation for the triggering information (cf.
>>> mne-python/mne/io/edf/tests/data/).
>>>
>>> Feel free to follow up and I can try to further debug this problem.
>>>
>>> Hope this helps,
>>>
>>>
>>> teon
>>> --
>>> Teon Brooks <http://teonbrooks.github.io>, PhD Candidate
>>> twitter: @teon_io <http://www.twitter.com/teon_io>
>>>
>>> On Sat, Jun 4, 2016 at 5:07 PM, David Soto <d.soto.b at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have data from  a study in which  Eprime was used  to send triggers
>>>> (integer numbers from 0-32) to the eeg system.
>>>> When I load the data using 'mne.io.read_raw_edf' and I try to load the
>>>> the trigger info  'mne.find_events(mydata)' I see only 5 digit numbers
>>>>  such as 65303, and even when I count the number of triggers of each type
>>>> it does not match what is expected.
>>>> I also tried to convert these numbers to 2 high and low byte numbers
>>>> but again the actual numbers and the amount do not match what is expected.
>>>> I have no idea what the problem is but I am sure the trigger info is well
>>>> contained in the  .bdf file, as a colleague of mine analysed this data for
>>>> a different research  purpose using Brain Vision Analyser. I am quite keen
>>>> on learning mne-python so any advise on how to load this trigger info would
>>>> be much appreciated.
>>>> In case it is useful a sample of the data can be downloaded here
>>>> https://drive.google.com/open?id=0B0PbSnFq24yMc2tKU29zWHZKRU0
>>>>
>>>> thanks!
>>>>
>>>> david
>>>>
>>>>
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