[FieldTrip] fieldtrip Digest, Vol 14, Issue 31

Fri Jan 20 19:06:29 CET 2012

Hi Robert

Thanks for your kind reply.

Best Regards,
Ayda
On Fri, Jan 20, 2012 at 6:00 AM, <fieldtrip-request at donders.ru.nl> wrote:

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> Today's Topics:
>
>   1. Re: ft_definetrial with .nex files (J?rn M. Horschig)
>   2. Re: ft_definetrial with .nex files (Robert Oostenveld)
>   3. Re: A problem (Robert Oostenveld)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 20 Jan 2012 09:48:18 +0100
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] ft_definetrial with .nex files
> Message-ID: <4F192A52.2050808 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Dear Tara,
>
> you define cfg.trialdef.triallength prior to calling ft_definetrial.
> This will cause the trialfunction to not look for events, but cut your
> recorded data into chunks of 3 seconds, independently of the eventtype
> and -value that you specified. The parameters you probably want to use
> instead are cfg.trialdef.poststim and .prestim. Triallength is supposed
> for continuous data without events, e.g. resting state data.
>
> Btw, if you specifiy cfg.trialdef.eventtype='?' you will get a list with
> all events in your data - that way you can make sure that you are
> specifying the correct types or values (alternatively, you could also
> use ft_read_event).
>
> Hope it helps!
> Best,
> J?rn
>
> On 1/19/2012 10:12 PM, Tara Jacobson wrote:
> > Hello,
> >
> > Does anyone have experience with .nex files?  It seems straight
> > forward to be able to define trials using events in the .nex, but
> > ft_definetrial is not recognizing them as events.
> >
> > filename =('11-087_12292011.nex')
> >
> >
> >
> stim30Hz=[27.25275159.26715258.277925357.2887489.303075522.306625621.317425786.335425885.3462984.3569751083.367751149.37491281.38931347.3964251446.407251578.42161644.42881776.4431751875.453951974.464725];
> >
> > cfg = [];
> > cfg.dataset = filename;
> >
> > cfg.trialdef.triallength=3;
> > cfg.trialdef.eventtype=('Event007');
> > cfg.trialdef.eventvalue=stim30Hz;
> >
> > cfg=ft_definetrial(cfg);
> >
> > filename =
> > 11-087_12292011.nex
> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 95
> > evaluating trialfunction 'trialfun_general'
> > reading the events from '11-087_12292011.nex'
> > found 0 events
> > created 676 trials
> >
> > My question is what are the 676 trials if it found no events?
> >
> > Can anyone give me some advice?
> >
> >
> > Thanks very much.
> >
> >
> >
> >
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>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
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> ------------------------------
>
> Message: 2
> Date: Fri, 20 Jan 2012 10:43:36 +0100
> From: Robert Oostenveld <r.oostenveld at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] ft_definetrial with .nex files
> Message-ID: <895F6559-E5B6-410F-B6AA-F8407C73E30F at donders.ru.nl>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Tara,
>
> To add to Jorns suggestion
>
> On 19 Jan 2012, at 22:12, Tara Jacobson wrote:
>
> > ...
> > cfg=ft_definetrial(cfg);
> >
> > filename =
> > 11-087_12292011.nex
> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 95
> > evaluating trialfunction 'trialfun_general'
> > reading the events from '11-087_12292011.nex'
> > found 0 events
> > created 676 trials
>
> The line "found 0 events" suggests that ft_read_event (which is called in
> ft_definetrial) did not find any events in your nex file. I suggest you
> look into the ft_read_event MATLAB code (and the underlying nex functions)
> to figure out why it does not detect the triggers in the nex file.
>
> best
> Robert
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 20 Jan 2012 10:49:59 +0100
> From: Robert Oostenveld <r.oostenveld at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] A problem
> Message-ID: <F6708862-5D39-4EBD-A9E5-9CC276910812 at donders.ru.nl>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Ayda
>
> On 19 Jan 2012, at 20:01, aida ghahremani wrote:
> > I have the coordinates of the cortex. Would you please help me to
> locates the sources (dipoles) which best explain the EEG?
>
> You can pass the cortical sheet to the ft_sourceanalysis function (or to
> the ft_prepare_leadfield function) to use all vertices of the cortical
> sheet as dipole locations. This is also the approach used in
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#source_model.
> The vertex positions should be specified as cfg.grid.pos.
>
> > How I can make their orientations normal to the cortex?
>
> You'll have to determine the dipole orientation at each vertex outside of
> fieldtrip, but you can use the fieldtrip/forward/private/normals.m to help
> you with it. If you specify the dipole orientations as cfg.grid.mom, then
> the leadfield will computed for a dipole in that direction. See line 227 in
> ft_prepare_leadfield.
>
> best
> Robert
>
>
>
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> End of fieldtrip Digest, Vol 14, Issue 31
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