[Mne_analysis] trigger information

Wed Apr 14 09:40:12 EDT 2010

Ricky, 
yet another way to view the stimulus channel would be to convert the raw data  into a Matlab .mat file
(using the mne_raw2mat commmand, see section 9.13 in the MNE Manual 2.6).

e.g. mne_raw2mat --raw <rawfilename> --mat <matfilename>

Then you can load the matfile, and plot and examine the stimulus channel (usually ch#313, but check MNE_raw_info). 
Or use the Matlab command unique(<stimchanneldatavector>), which will give you all the different pulse values recorded on the stimulus channel.
They should include your condition/trial triggers and the response button values.
Kestas

On Apr 5, 2010, at 4:07 PM, rsachdev at nmr.mgh.harvard.edu wrote:

> Thank you for the help, but I don't think it is a syntax issue.  It is
> more... did the scanner store the button responses in the STI channel. 
> When I run the command, it writes out the .eve file with relevant
> information. It is just missing the critical button response information.
> Is there another way to process the raw file and hopefully extract the
> response triggers?  Mne_browse_raw also shows no response triggers.
> 
> 
> -Ricky
> 
> 
>> Hi Ricky,
>> 
>> I think the problem may be a simple syntax issue.
>> 
>> The first question to answer is is there a triggers directory in the
>> directory you run the command from? (i.e. can you "ls ./triggers/")
>> 
>> Is the file written?
>> 
>> If the answers to these are "Yes" and "no", try using "./triggers/
>> CPLEX_01_V12.eve" instead of without the "./". You may want to
>> consider using the full path to data in future calls to commands to
>> avoid issues like these (environment variables can be very helpful
>> for keeping these simple).
>> 
>> Good Luck!
>> Dan
>> 
>> On 5 Apr 2010, at 20:41, rsachdev at nmr.mgh.harvard.edu wrote:
>> 
>>> output:
>>> mne_process_raw version 2.28 compiled at Dec 15 2009 08:56:37
>>> 64-bit architecture. Using 2000.00 Mbytes for ring buffers
>>> 
>>> --- Setting up the filter ---
>>> 
>>> Using a 4096-point FFT in filtering of raw data with 2048-sample
>>> tapers
>>> bandpass =    0.0 (   0.0) ...   40.0 (   5.0) Hz
>>> filter is on
>>> 
>>> --- Opening raw_data/CPLEX_01_V1_raw.fif ---
>>> 
>>> No compensation data in raw_data/CPLEX_01_V1_raw.fif
>>> Compensation in file : uncompensated
>>> Setting up compensation data...
>>>        No compensation set. Nothing more to do.
>>> No compensation was requested.
>>> A new compensation value (uncompensated) was assigned to 306 MEG
>>> channels.
>>> No SSS data in raw_data/CPLEX_01_V1_raw.fif
>>> Data skip of 22800 samples in the beginning
>>> 0 bad channels read from raw_data/CPLEX_01_V1_raw.fif
>>> filter :   0.000 ...   40.0 Hz   bins : 0 ... 545 of 4097 hpw : 3
>>> lpw : 34
>>> Highpass filter will work as specified.
>>> Initial dc offsets determined
>>> Raw data file raw_data/CPLEX_01_V1_raw.fif:
>>>        nchan  = 389
>>>        nsamp  = 143400
>>>        sfreq  = 600.615  Hz
>>>        length = 238.755  sec
>>> 268 events found in raw_data/CPLEX_01_V1_raw-eve.fif
>>> Trigger channel : STI 014 max_event : 41
>>> 
>>> --- Saving events (leading edge) in text format to
>>> triggers/CPLEX_01_V12.eve ---
>>> 
>>> 
>>> --- Complete ---
>>> 
>>> -Ricky
>>> 
>>> 
>>> 
>>>> What was the output when you ran the command?
>>>> 
>>>> 
>>>> On 5 Apr 2010, at 20:33, rsachdev at nmr.mgh.harvard.edu wrote:
>>>> 
>>>>> Sorry about that.
>>>>> 
>>>>> 1.MNE 2.7
>>>>> 2.the command was mne_process_raw --raw raw_data/raw.fif --eventsout
>>>>> triggers/.eve
>>>>> 3.The data was along the lines of this:
>>>>> 22800 37.961       0   0
>>>>> 25252 42.044       0  41
>>>>> 26547 44.200       0  11
>>>>> 27674 46.076       0   2
>>>>> 28793 47.939       0   8
>>>>> 29898 49.779       0   3
>>>>> 30983 51.585       0   9
>>>>> 32118 53.475       0  14
>>>>> 33298 55.440       0  19
>>>>> 34436 57.335       0  20
>>>>> 35508 59.119       0  16
>>>>> 36649 61.019       0  13
>>>>> 37756 62.862       0  11   %The button presses are assigned trigger
>>>>> values 64 and 128 (channels 7 and 8).  A button response was
>>>>> supposed to
>>>>> be recorded after onset of every stimuli and every stimuli was
>>>>> assigned a
>>>>> trigger number as shown above.
>>>>> 4. It was from Charlestown
>>>>> 5.  No special setting were used during data collection or when
>>>>> running
>>>>> the command.
>>>>> 
>>>>> Thank you,
>>>>> -Ricky
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> Hi Ricky,
>>>>>> 
>>>>>> Can you provide us with some more information? We can't help
>>>>>> without
>>>>>> some more details like:
>>>>>> 
>>>>>> What version of MNE?
>>>>>> What was the exact command run?
>>>>>> What was the output of that command?
>>>>>> What system did the data come from (I assume the Charlestown one)?
>>>>>> Did you employ any special settings when collecting the data?
>>>>>> Did you employ any special settings in your environment, when
>>>>>> running
>>>>>> the command (e.g. MNE_TRIGGER_CH_NAME)?
>>>>>> 
>>>>>> Thanks
>>>>>> Dan
>>>>>> 
>>>>>> On 5 Apr 2010, at 20:10, rsachdev at nmr.mgh.harvard.edu wrote:
>>>>>> 
>>>>>>> Hello,
>>>>>>> 
>>>>>>> After running mne_process_raw --raw <raw> --eventsout <output>, I
>>>>>>> wasn't
>>>>>>> able to find the trigger code for the button presses in the event
>>>>>>> file.  I
>>>>>>> don't know if it wasn't recorded and stored during the MEG scan or
>>>>>>> if I
>>>>>>> made a mistake on my part.
>>>>>>> 
>>>>>>> Any input is appreciated.
>>>>>>> 
>>>>>>> Thank you,
>>>>>>> -Ricky
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>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
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