[FieldTrip] working with neuromag data
Stolk, A.
a.stolk at fcdonders.ru.nl
Thu Jun 16 20:33:38 CEST 2011
Dear Kambiz,
To answer your first question, I do not know what this error when calling ft_topoplotER means.
Secondly, ft_multiplotTFR is a visualization step of the data and not an analysis step. It is not necessary to call this function before proceeding, but giving that it works far from what you'd expect, it tells us something's wrong. :)
At your third question; what do you mean with layout information? Information on the gradiometer and magnetometer definitions? Keep in mind that when creating a grand-average, you cannot effectively average these.
Ok, for a plan de campagne; are you using the most recent version of FT? If so, could you send me your data in a .mat file? Please send it to my e-mail address and not the FT list.
Yours,
Arjen
Are you using the most recent version of FT?
----- "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: Donderdag 16 juni 2011 18:31:54
> Onderwerp: Re: [FieldTrip] working with neuromag data
>
> 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
> > _______________________________________________
> > 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
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
More information about the fieldtrip
mailing list