[FieldTrip] working with neuromag data

Tavabi, Kambiz TAVABIK at email.chop.edu
Fri Jun 10 20:21:30 CEST 2011 

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?

Following up my question on plotting: Why would the granaverge structure lose the channel layout information instead of carrying it over from the Timelock structure?
ft_topoplotER(cfg,grandavgc1)
??? Error using ==> ft_prepare_layout at 532
no layout detected, please specify cfg.layout

Error in ==> ft_topoplotER at 408
lay = ft_prepare_layout(cfg, data);

-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
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> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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