[Mne_analysis] trigger information
Adrian KC Lee
akclee at nmr.mgh.harvard.edu
Mon Apr 5 16:45:00 EDT 2010
Hi Ricky
Did you see the buttons triggered in your acquisition? Sometimes, when
people use the MEG at Martinos, they don't switch back Ch.5-8 to the
correct (hold "hi" configuration... see the diagram on the side of the
equipment rack). If that was not in that configuration and if you
don't see the pulses when you acquire, then you basically didn't
record the responses.
Hope this helps.
Cheers
KC
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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Adrian KC Lee, ScD
Instructor
Radiology at Harvard Medical School
Department of Radiology, MGH
Athinoula A. Martinos Center for Biomedical Imaging
Research Associate
Department of Cognitive & Neural Systems, Boston University
Director of BAMBI
Boston-Area Machine-Brain Interfaces outreach program
National Science Foundation Science of Learning Center
Center of Excellence for Learning in Education, Science and Technology
Email: akclee at alum.mit.edu
Website: www.akclee.com
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