[Mne_analysis] mne_process_raw: event extraction

[Hari Bharadwaj]

Hi Reid,
  If you recorded at the Martinos center, try STI102 instead of STI101 to
see if your triggers are there..

Regards,
Hari



On Tue, September 25, 2012 11:52 am, Eric Larson wrote:
> I'd suggest loading up MATLAB (or Python, the code will be very
> similar) and trying something like this:
>
> inFile = fullfile('raw_dir','MVS1_12_B8_raw.fif');
> raw = fiff_setup_read_raw(inFile,true)
> STIInd = find(~cellfun(@isempty,strfind(raw.info.ch_names,'STI101')));
> picks = fiff_pick_channels(raw.info.ch_names,[],[]);
> data = fiff_read_raw_segment(raw,raw.first_samp,raw.last_samp,picks);
> trigData = data(STIInd,:);
>
> Then your trigger channel data should be in "trigData". This way you
> can also manually examine raw.info.ch_names to see what it's called,
> and once you find it, you can look at the raw data to see what's going
> on. I had a problem at one point where a high bit (32 I think?) was
> stuck on, so no lower-value events (1/2/4/8) were detected, so I had
> to pull them out of the raw data myself with a script. Hopefully
> that's not your issue, but it could be.
>
> Eric
>
>
>
> On Tue, Sep 25, 2012 at 8:41 AM, Vancelette, Reid Vincent
> <RVANCELETTE at partners.org> wrote:
>> Hi all again,
>>
>> Thanks for all your responses. I have tried with/without spaces, and/or
>> underscores, and with single quotes and none of these options allows me
>> to get the channels. I still get this readout:
>>
>> 0 events found in /autofs/space/.../raw_data/MVS1_12_B8_raw-eve.fif
>> Trigger channel : STI101 max_event : 0
>>
>> -Reid
>>
>> -----Original Message-----
>> From: Eric Larson [mailto:larson.eric.d at gmail.com]
>> Sent: Tuesday, September 25, 2012 11:17 AM
>> To: Vancelette, Reid Vincent
>> Cc: mne_analysis at nmr.mgh.harvard.edu
>> Subject: Re: [Mne_analysis] mne_process_raw: event extraction
>>
>> Hey Reid,
>>
>> We also use STI101. Depending on how the channel is actually named, you
>> might not need that underscore and should use
>>
>> --digtrig 'STI101'
>>
>> That's what works for us---single quotes on each side, no spaces---but
>> you might need to adjust with/without spaces and/or underscores based on
>> how your system actually names that channel.
>>
>> Cheers,
>> Eric
>>
>>
>> On Tue, Sep 25, 2012 at 7:50 AM, Vancelette, Reid Vincent
>> <RVANCELETTE at partners.org> wrote:
>>> Hi group,
>>>
>>>
>>>
>>> I have been trying to extract events from my raw data with the
>>> mne_process_raw command. I have changed the STI channel from STI 014
>>> to
>>> STI101 per Matti's instructions:
>>>
>>>
>>>
>>> 'mne_process_raw --raw %s/raw_data/%s_%s_raw.fif --eventsout
>>> %s/triggers/%s_%s.eve --digtrig STI_101'
>>>
>>>
>>>
>>> and 0 events are extracted. I receive the following message:
>>>
>>>
>>>
>>> 0 events found in /autofs/space/.../raw_data/MVS1_12_B8_raw-eve.fif
>>> Trigger channel : STI 101 max_event : 0
>>>
>>> --- Saving events (leading edge) in text format to
>>> /autofs/space/.../triggers/MVS1_12_B8.eve ---
>>>
>>> No events to save
>>>
>>>
>>>
>>> I have looked into the raw fif files to check to see whether or not
>>> the triggers were recorded and they were. Is there something else that
>>> I need to do/define in order to extract the events successfully?
>>>
>>>
>>>
>>> Thanks in advance again,
>>>
>>>
>>>
>>> Reid
>>>
>>>
>>>
>>>
>>>
>>>
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-- 
Hari Bharadwaj
PhD Candidate, Biomedical Engineering,
Boston University
677 Beacon St.,
Boston, MA 02215

Martinos Center for Biomedical Imaging,
Massachusetts General Hospital
149 Thirteenth Street,
Charlestown, MA 02129

hari at nmr.mgh.harvard.edu
Ph: 734-883-5954