[Mne_analysis] mne_process_raw: event extraction

Eric Larson larson.eric.d at gmail.com
Tue Sep 25 11:52:14 EDT 2012
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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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