[Mne_analysis] Grand Averaging from Text Events Files

Wed Jan 25 16:43:15 EST 2012

Hey Brian Dan and MNErs,

I think you may be misinterpreting the event files.

Take for instance the first three lines of a event file I have:

 19800 32.966       0   0
 20740 34.531       0  36
 21446 35.707       0 128

* The first column is the sample number (which is dependent on the sample
rate, for this subject it is 600.615 Hertz) since I pressed the GO button
on the MEG machine (I didn't click the record raw button until 32 seconds
in because I was writing the HPI coordinates, 19800 samples in)
* The second column is the seconds since GO
* The third is the channel STI 014 base (always 0)
* The fourth is the channel's increase to (which should correspond to the
trigger number you gave it).

Check out the manual for more details.

http://martinos.org/mne/manual/browse.html#event-files

Does this explain the weirdness in the files?

- Conrad

> Hello again,
>
> On Wed, Jan 25, 2012 at 1:50 PM, Dan Wakeman <dgwakeman at gmail.com> wrote:
>
>> On Wed, Jan 25, 2012 at 3:38 PM, Brian Coffman <bcoffman at mrn.org> wrote:
>> > Hi Conrad,
>> > Thanks for your help. This looks a bit complex for what we are doing.
>> We
>> > already get the events we are interested when averaging without
>> corrections
>> > by specifying --eventsout within mne_process_raw. These files come out
>> with
>> > an initial skip (offset) value in the form of "seconds milliseconds 0
>> 0." It
>> > seems after a bit more testing that this initial skip is not accounted
>> for
>> > when averaging from the events files that come out of MNE.
>> How did you test this? We need to understand what tests you are doing
>> to understand why you think it is "not accounted for."
>>
> When averaging directly from the events file that MNE has generated (using
> --eventsout) in a file with an initial skip of 4 seconds, I get a .fif and
> a .log file that together suggest that MNE is averaging 4 seconds later
> than it should, as if the first line of the events file is disregarded
> during averaging.
>
>>
>> > I have started to use the log file timing for the first run (log files
>> seem
>> > to contain timing relative to the start of the .fif file, while the
>> events
>> > files contain timing for the entire dataset, with an initial skip at
>> the
>> > beginning of the file) and this works fine. This doesn't work for the
>> 2nd
>> > and 3rd file, though, as MNE looks for the dataset event time rather
>> than
>> > the fif file event time. Using the events file timing for the second
>> and
>> > third runs seems to work just fine, with or without the initial skip.
>> >
>> > It seems very strange that MNE would write events in a way that can't
>> be
>> > read for averaging. Is this possibly related to the version of MNE I
>> am
>> > using (2.7.3)?
>>
>> How is MNE writing events in a way that can't be used for averaging?
>> Can you explain what this means?
>>
>
> The event times in the --eventsout file are equal to the event times in
> the
> log file + the initial skip. If the initial skip were taken into
> consideration and subtracted from the event times that follow when
> averaging, then one would get the correct event times, however, this does
> not seem to be the case. The log file from an average using the event file
> generated by MNE shows events are off by 4 seconds (the initial skip) and
> are in fact the event times listed in the event file. The log file from an
> average without specifying an event file shows the correct event times.
>
>>
>> Dan
>> >
>> > On Wed, Jan 25, 2012 at 1:08 PM, <conrad at nmr.mgh.harvard.edu> wrote:
>> >>
>> >> Brian,
>> >>
>> >> I'm not sure why you need to change the events by an offset. I'll
>> explain
>> >> my approach to the same problem (rewriting new .eve files based on
>> subject
>> >> criteria eg. correctness). From your description, I am not sure what
>> you
>> >> mean by offsets, and I think if your triggers were at the right times
>> you
>> >> don't want to rewrite or readd any offsets just use the original
>> event
>> >> timing. (If you do want to change the timing of triggers that is
>> another
>> >> problem my lab has to deal with. We have a solution but haven't
>> tested
>> it
>> >> out yet)
>> >>
>> >> I contain all of my subject (and study) variables in structures,
>> hopefully
>> >> their syntax is intuitive so I don't need to explain it. I do this in
>> >> Matlab, but if you use a different programming environment I may be
>> able
>> >> to help you translate.
>> >>
>> >> Presume we have already extracted event files from each of the raw
>> data
>> >> blocks.
>> >>
>> >> > event_file = sprintf('%s/triggers/%s_%s.eve',...
>> >> >   subject.meg.dir, subject.name, block);
>> >> > events = load(event_file);
>> >>
>> >> Matlab's load command loads them perfectly. Now events is a N row by
>> 4
>> >> column matrix representing the data from the .eve file. Then my code
>> goes
>> >> line by line, finding events that correspond to triggers we sent and
>> the
>> >> next user input and evaluates their action. For events that we will
>> use
>> in
>> >> the analysis I reassign by:
>> >>
>> >> > events(i, 4) = some_code;
>> >>
>> >> I do not delete events I will not use. I presume you still could by
>> doing:
>> >>
>> >> > events(i, :) = [];
>> >> or just make a new events matrix for ones you will include
>> >> > new_events(end + 1, :) = events(i, :);
>> >> just make sure to include the initial line before you do that
>> >> > new_events(1, :) = events(1, :);
>> >>
>> >> Then I make a new event_file and reprint every line based on the
>> events
>> >> matrix.
>> >>
>> >> > event_file = sprintf('%s/triggers/%s_%s_applied.eve',...
>> >> >   subject.meg.dir, subject.name, block);
>> >> > fid = fopen(event_file);
>> >> > for i = 1:size(events, 1)
>> >> >   fprintf(fid, '%6d %3.3f %6d %3d\n',...
>> >> >     events(i, 1), events(i, 2), events(i, 3), events(i, 4));
>> >> > end
>> >> > fclose(fid);
>> >>
>> >> I hope that makes some sense and could be useful. Good luck with it!
>> >>
>> >> - Conrad Nied
>> >> Neuropsychology Lab @ MGH, David Gow
>> >> 617 724 8846
>> >> conrad at martinos.org
>> >>
>> >> > Hello MNE users,
>> >> > I am having an odd issue that I am having trouble conceptualizing.
>> >> >
>> >> > I am averaging data that is split into 3 raw data files, then
>> taking
>> the
>> >> > events files generated from these averages and modifying these
>> events
>> >> > files
>> >> > to include only events where the subject responded correctly. I am
>> then
>> >> > taking these corrected events files and grand averaging the raw
>> data
>> to
>> >> > end
>> >> > up with a single .fif average which is corrected for our behavioral
>> >> > data.
>> >> >
>> >> > The issue I am having is related ot the initial offsets in the
>> events
>> >> > files. In all cases, there is an initial offset greater than zero
>> for
>> >> > the
>> >> > 2nd and 3rd raw data files. In some cases, there is also an initial
>> >> > offset
>> >> > of a few seconds in the events file for the first of the three raw
>> data
>> >> > files. It seems from the log files that the offset is being
>> utilized
>> >> > differently for the two cases (a few seconds offset vs a whole
>> dataset
>> >> > offset). For the log from the first file, the offset is added to
>> the
>> >> > times,
>> >> > while for the other files, the offset is not added. For example,
>> with
>> an
>> >> > initial offset of 4 seconds, the log for the uncorrected average
>> starts
>> >> > at
>> >> > 29.555 seconds, while for the corrected data, the log starts at
>> 33.555
>> >> > seconds. The logs are identical for the second and third data
>> files.
>> >> > This
>> >> > is also apparent in the averages, as there is no signal in the
>> corrected
>> >> > average of the first raw file. It seems that the offsets are
>> necessary
>> >> > for
>> >> > the later files (data files 2 and 3), however, as I get no averages
>> >> > without
>> >> > them.
>> >> >
>> >> > My question is: Should I eliminate these offsets from the first
>> text
>> >> > events
>> >> > file when averaging from events files? Is there something I have
>> not
>> >> > considered here?
>> >> >
>> >> >
>> >> > Thanks in advance!!
>> >> >
>> >> > -Brian Coffman, M.S.
>> >> > Research Associate, The Mind Research Network
>> >> > Doctoral Candidate, The University of New Mexico
>> >> >
>> >> > Phone: (505) 336-0606
>> >> > Fax: (505) 272-7011
>> >> >
>> >> > "I used to think that the brain was the most wonderful organ in my
>> body.
>> >> > Then I realized who was telling me this."
>> >> >   - Emo Phillips
>> >> > _______________________________________________
>> >> > Mne_analysis mailing list
>> >> > Mne_analysis at nmr.mgh.harvard.edu
>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>
>> >>
>> >>
>> >> The information in this e-mail is intended only for the person to
>> whom
>> it
>> >> is
>> >> addressed. If you believe this e-mail was sent to you in error and
>> the
>> >> e-mail
>> >> contains patient information, please contact the Partners Compliance
>> >> HelpLine at
>> >> http://www.partners.org/complianceline . If the e-mail was sent to
>> you
>> in
>> >> error
>> >> but does not contain patient information, please contact the sender
>> and
>> >> properly
>> >> dispose of the e-mail.
>> >>
>> >
>> >
>> >
>> > --
>> > -Brian Coffman, M.S.
>> > Research Associate, The Mind Research Network
>> > Doctoral Candidate, The University of New Mexico
>> >
>> > Phone: (505) 336-0606
>> > Fax: (505) 272-7011
>> >
>> > "I used to think that the brain was the most wonderful organ in my
>> body.
>> > Then I realized who was telling me this."
>> >   - Emo Phillips
>> >
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> in
>> > error
>> > but does not contain patient information, please contact the sender
>> and
>> > properly
>> > dispose of the e-mail.
>> >
>>
>
>
>
> --
> -Brian Coffman, M.S.
> Research Associate, The Mind Research Network
> Doctoral Candidate, The University of New Mexico
>
> Phone: (505) 336-0606
> Fax: (505) 272-7011
>
> "I used to think that the brain was the most wonderful organ in my body.
> Then I realized who was telling me this."
>   - Emo Phillips
>