[Mne_analysis] Grand Averaging from Text Events Files

Wed Jan 25 16:19:02 EST 2012

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
> >>
> >>
> >>
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> >> is
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> >
> >
> >
> > --
> > -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
> >
> >
> > _______________________________________________
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> > 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
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> in
> > error
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> >
>

-- 
-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
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