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

David Soto d.soto.b at gmail.com
Mon Jun 13 03:42:46 EDT 2016
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HI Teon, thanks this seems to do the job!
best
david

On 7 June 2016 at 16:30, Teon Brooks <teon.brooks at gmail.com> wrote:

> Hi David,
>
> The 32 refers to the bit mask that you want. I think you would be safe
> with using 2**17 - 256. Below is the code snippet of what I did. Do you
> expect there to be 2000 events total?
>
> In [1]: raw =
> mne.io.read_raw_edf('/Users/teon/Downloads/AnnaPriming.bdf',
> stim_channel=-1)
>
> Extracting edf Parameters from /Users/teon/Downloads/AnnaPriming.bdf...
>
> Setting channel info structure...
>
> Creating Raw.info structure...
>
> Ready.
>
>
> In [2]: mne.find_events(raw, mask=2**17 -256)
>
> Removing orphaned offset at the beginning of the file.
>
> 2000 events found
>
> Events id: [ 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21
> 22 23 24 25
>
>  26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 47 63 64]
>
> Out[2]:
>
> array([[   1550,       0,      25],
>
>        [   1942,      25,      27],
>
>        [   2352,       0,      27],
>
>        ...,
>
>        [1100573,      31,      63],
>
>        [1100982,       0,      33],
>
>        [1101254,       0,      34]])
>
>
>
>
> teon
> --
> Teon Brooks <http://teonbrooks.github.io>, PhD Candidate
> twitter: @teon_io <http://www.twitter.com/teon_io>
>
> On Sun, Jun 5, 2016 at 5:59 PM, David Soto <d.soto.b at gmail.com> wrote:
>
>> 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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