[FieldTrip] working with neuromag data

[Tavabi, Kambiz]

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