[FieldTrip] working with neuromag data

Tavabi, Kambiz TAVABIK at email.chop.edu
Thu Jun 16 18:31:54 CEST 2011 

Dear Arjen, 
The data.avg I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings:
1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719
2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? 

>From what I understand the ft_multiplotER step is necessary to carry out sensor level analysis of the data? 

As I mentioned previously, the grand average data structure does not contain the proper layout information that is in the timelock structure. Is this purposefully done, or am I doing something wrong here?

Regards,

-Kambiz.
-------------------------------------------------------------
Kambiz Tavabi PhD
Biomedical Imaging Laboratory
The Children's Hospital of Philadelphia
34th Street and Civic Center Boulevard
Philadelphia, Pa. 19104
Tel: 267.426.0302
email: tavabik at email.chop.edu
-------------------------------------------------------------
________________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl]
Sent: Saturday, June 11, 2011 3:26 AM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] working with neuromag data

Dear Kambiz,

Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim?

Yours,
Arjen

----- "Kambiz Tavabi" <TAVABIK at email.chop.edu> schreef:

> Van: "Kambiz Tavabi" <TAVABIK at email.chop.edu>
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Verzonden: Vrijdag 10 juni 2011 18:59:03
> Onderwerp: Re: [FieldTrip] working with neuromag data
>
> As per advise from Arjen, I was able to use following steps
> 1) ft_preprocessing on your stimulus averaged epoch data. This should
> give you a data structure with 6 trials (which are actually the
> averages per condition).
> 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat
> this so you end up with 6 timelocked structures representing the 6
> different conditions.
> to create individual condition averaged ft data structures which I can
> visualize using ft_topoplotER(cfg,data)
> data:
> avg: [338x651 double]
>         var: [338x651 double]
>     fsample: 1000
>        time: [1x651 double]
>         dof: [338x651 double]
>       label: {338x1 cell}
>      dimord: 'chan_time'
>        grad: [1x1 struct]
>         cfg: [1x1 struct]
> however when i use;
> cfg = [];
> cfg.showlabels = 'yes';
> cfg.fontsize = 6;
> cfg.ylim = [-10e-13 10e-13]
> ft_multiplotER(cfg, data);
> Fieldtrip chruns through creating the
> selection avg along dimension 1
> selection dof along dimension 1
> selection var along dimension 1
> creating layout from data.grad
> creating layout for neuromag306 system
>
> but the resutling figure is an empty figure containing only layout
> with ch lables without any data what so ever. Any ideas why this might
> be?
>
>
>
> -Kambiz.
> -------------------------------------------------------------
> Kambiz Tavabi PhD
> Biomedical Imaging Laboratory
> The Children's Hospital of Philadelphia
> 34th Street and Civic Center Boulevard
> Philadelphia, Pa. 19104
> Tel: 267.426.0302
> email: tavabik at email.chop.edu
> -------------------------------------------------------------
> ________________________________________
> From: fieldtrip-bounces at donders.ru.nl
> [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A.
> [a.stolk at fcdonders.ru.nl]
> Sent: Tuesday, March 29, 2011 4:20 AM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] working with neuromag data
>
> Dear Kambiz,
>
> I think I see your point. Your data presumably is already preprocessed
> and timelocked (averaged over trials) with neuromag software. I then
> take it that you have 6 different conditions which you would like to
> plot separately and possibly test at the group level.
>
> Since the data is already averaged, I'd recommend to do the following
> to get your data back on track.
>
> 1) ft_preprocessing on your stimulus averaged epoch data. This should
> give you a data structure with 6 trials (which are actually the
> averages per condition).
>
> 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat
> this so you end up with 6 timelocked structures representing the 6
> different conditions.
>
> 3) plot or grandaverage (see tutorials how to proceed as your data now
> should be 'ft-friendly').
>
> Goodluck,
> Arjen
>
>
>
>
>
>
> ----- "Kambiz Tavabi" <TAVABIK at email.chop.edu> schreef:
>
> > Van: "Kambiz Tavabi" <TAVABIK at email.chop.edu>
> > Aan: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> > Verzonden: Dinsdag 29 maart 2011 01:10:14
> > Onderwerp: Re: [FieldTrip] working with neuromag data
> >
> > Dear Arjen - Thanks for your response. Just to clarify the low
> level
> > functions ft_read_header & ft_read_data are mentioned in the ft
> > getting started tutorial. I believe they're recommended to make
> sure
> > the data is ft friendly. In my case the data is ft friendly. My
> data
> > is also pre-processed and already 'time-locked'--meaning that I
> have
> > stimulus averaged epoch data in fif format for all my subjects. My
> > question is how to proceed from there? I've been through the pages
> you
> > refer to but have not been able to piece together my data in such a
> > way to proceed with grand-averaging and carrying out stats.
> > -Kambiz.
> > -------------------------------------------------------------
> > Kambiz Tavabi PhD
> > Biomedical Imaging Laboratory
> > The Children's Hospital of Philadelphia
> > 34th Street and Civic Center Boulevard
> > Philadelphia, Pa. 19104
> > Tel: 267.426.0302
> > email: tavabik at email.chop.edu
> > -------------------------------------------------------------
> > ________________________________________
> > From: fieldtrip-bounces at donders.ru.nl
> > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A.
> > [a.stolk at fcdonders.ru.nl]
> > Sent: Monday, March 28, 2011 4:05 PM
> > To: Email discussion list for the FieldTrip project
> > Subject: Re: [FieldTrip] working with neuromag data
> >
> > Dear Kambiz,
> >
> > While you are able to use the 'low level' ft_read_header and
> > ft_read_data functions, you should be able to preprocess and
> analyze
> > your neuromag data using the 'high level' functions such as
> > ft_preprocessing (which calls the low level functions mentioned
> > above).
> >
> > How to proceed depends on what you want to do with your data. If
> you
> > have triggers stored in your dataset that are synchronuous with the
> > recorded brain activity, it'd be recommended to start with the
> > following tutorial on how to select your trials:
> >
> > http://fieldtrip.fcdonders.nl/tutorial/preprocessing
> >
> > Since your experience with FT is still limited as you say, I
> believe
> > the following text may provide a good overview of what the data,
> once
> > read in to FT (i.e. matlab) environment, may look like:
> >
> > http://fieldtrip.fcdonders.nl/walkthrough
> >
> > Typically, your next steps involve single-subject timelocked
> analysis,
> > then grand-average and perform statistics at the group level. For
> an
> > overview of the steps and protocols, see:
> >
> > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols
> >
> > Hope this has helped for a start,
> >
> > Arjen
> >
> >
> > ----- "Kambiz Tavabi" <TAVABIK at email.chop.edu> schreef:
> >
> > > Van: "Kambiz Tavabi" <TAVABIK at email.chop.edu>
> > > Aan: "Email discussion list for the FieldTrip project"
> > <fieldtrip at donders.ru.nl>
> > > Verzonden: Maandag 28 maart 2011 20:59:36
> > > Onderwerp: [FieldTrip] working with neuromag data
> > >
> > > Greetings - I have preprocessed/averaged neuromag data for a
> group
> > of
> > > subjects that I'd like to visualize, compute grandaverage and
> carry
> > > out sensor level statistics on. The only help I managed to find
> on
> > the
> > > Fieldtrip site/list Re: neurmag data concerns getting started
> e.g.,
> > > with ft_read_header and ft_read_data. In my case these programs
> > work
> > > fine meaning that I can proceed with further analysis.
> > > On a side, in my limited experience with FT, a major problem I
> run
> > > into frequently is that there is no clear suggestion(s) on how to
> > > proceed with data that is not raw. I understand it is impossible
> to
> > > cover all analysis scenarios, but it is often the case that
> working
> > > with CTF, or in particular Elekta system, the data is likely to
> be
> > in
> > > a post-preprocessed phase. Everytime I've tried to work with ft,
> It
> > > seems to me that if I don't start with square one in fieldtrip,
> it
> > is
> > > difficult to figure out how to use downstream programs to work on
> > the
> > > data.
> > > That said, in my case I have the output from ft_read_header:
> > >
> > > label: {338x1 cell}
> > >          nChans: 338
> > >              Fs: 1000
> > >            grad: [1x1 struct]
> > >            unit: {1x338 cell}
> > >        nSamples: 651
> > >     nSamplesPre: 100
> > >         nTrials: 6
> > >            orig: [1x1 struct]
> > >
> > > and output from ft_read_data
> > >
> > > [338x651x6] that being channels by samples by number of stimulus
> > > averaged epochs. To proceed, ideally I'd like to compute a
> > > grandaverage for each condition, visualize them in a multiplot,
> and
> > > carry out sensor level stats. To be able to do this I understand
> I
> > > need the output from ft_timelockanalysis, how do I arrange my
> data
> > as
> > > such? I am assuming it is already in that state. Thanks for your
> > > time.
> > >
> > > -Kambiz.
> > > -------------------------------------------------------------
> > > Kambiz Tavabi PhD
> > > Biomedical Imaging Laboratory
> > > The Children's Hospital of Philadelphia
> > > 34th Street and Civic Center Boulevard
> > > Philadelphia, Pa. 19104
> > > Tel: 267.426.0302
> > > email: tavabik at email.chop.edu
> > > -------------------------------------------------------------
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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