[Mne_analysis] trouble reading the triggers in a .BDF file
Teon Brooks
teon.brooks at gmail.com
Tue Jun 7 10:30:18 EDT 2016
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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