[FieldTrip] A question

Stephen Politzer-Ahles politzerahless at gmail.com
Thu Feb 16 12:35:13 CET 2012


Hi Shayda,

FieldTrip does not apply a filter by default, and I am not aware of any
other 'hidden' transformations that happen. You can specify a filter when
importing the data with ft_preprocessing(), and there are several different
kinds of filters available, which will affect your data in different ways--
see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best
thing to do is to import your data without using a filter and, if possible,
use whatever tool comes with your MEG software to import that raw data into
MATLAB as well (for example, for CTF this would be ds2txt), then you can
plot them together to make sure there are no differences--when I have tried
this with EEG data, fieldtrip hasn't changed them. Of course, if you want
to use a filter, you can also try several filters (you can either filter
within your system's software and then import straight to Fieldtrip, or use
one of Fieldtrip's filters during import) and plot them to see how they
affect your data.

Best,
Steve Politzer-Ahles



>
> Message: 2
> Date: Wed, 15 Feb 2012 14:19:50 -0600
> From: Shayda Malekpour <shayda.malekpour at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] A question
> Message-ID:
>        <CAMUfAt=cGAnjLDby96CnXi4ubV=v2RCDnM9HoH2ObG5ZT5Bdeg at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
>
> I am using fieldtrip on MEG data set.
> I want to know if I do not remove any ICA component,  will the data be  the
> same as the original data, or is there is a filter somewhere in the
> software that changes the data? If so how much does it change it (What is
> their relative difference?)
>
> Thanks,
>
> Sheida
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> Message: 3
> Date: Thu, 16 Feb 2012 09:28:43 +0100
> From: Eelke Spaak <eelke.spaak at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] A question
> Message-ID:
>        <CABPNLUp8hQFKG7d1cuUQt4rkb3mfqxtqDWk4AyKrf5ZX8b3BYA at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Sheida,
>
> You probably need to provide a bit more information before anyone is
> able to help you. In general, if you perform ICA, you get out
> component timecourses and mixing/unmixing matrices. If you keep all
> your components, and multiply them with the mixing matrix, you should
> get all your original channel timecourses out again. So: if you don't
> change the data, the data will not be changed :)
>
> Best,
> Eelke
>
> On 15 February 2012 21:19, Shayda Malekpour <shayda.malekpour at gmail.com>
> wrote:
> > Dear All,
> >
> > I am using fieldtrip on MEG data set.
> > I want to know if I do not remove any ICA component,? will the data be?
> the
> > same as the original data, or is there is a filter somewhere in the
> software
> > that changes the data? If so how much does it change it (What is their
> > relative difference?)
> >
> > Thanks,
> >
> > Sheida
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 16 Feb 2012 10:36:05 +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] A problem in real-time processing of MEG
>        signal using field trip buffer
> Message-ID: <4F3CCE05.4050109 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Dear Soheila,
>
> we were facing the same problem here. Presumably, there is some problem
> in the shared memory module that the buffer is using. Right now,
> however, we could not find out where the error precisely comes from, so
> our best work around is to restart the computer prior recording and
> optimize settings, such as channels and sampling/decimation rate of
> acq2ft. In our lab, we managed to find near-optimal settings, so that
> the buffer crashes only rarely (actually, I never saw it crashing when
> the acquisition computer was freshly restarted). Note that a lower
> number of channels or higher decimation does not mean that it runs more
> stable.  It seems to be literally a trial-and-error approach :/
>
> In order to track this down further, we need some more information, e.g.
> what MEG system are you using? What's your sampling rate, how many
> channels do you put into the buffer, and what's your decimation rate? It
> would be great if you could send me that information so that we can
> maybe try to track this down.
>
> Best regards,
> J?rn
>
> On 2/14/2012 5:42 PM, Soheila Samiee wrote:
> > Dear group,
> >
> > I use FieldTrip for real-time processing of MEG signals using shared
> > memory and field trip buffer in a machine other than acquisition
> > system. I use matlab for reading the buffer and processing the data.
> > During my data acquisition and sending it to other computer with
> > /acq2ft/ in linux, I face a problem. After sending some blocks of
> > data, this message: "/Internal Converter thread does not keep up with
> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I
> > see an error : "ERROR: the buffer returned an error (517)". It does
> > not depend on sampling rate of data in acquisition system. The problem
> > often solve when I restart the computer which receives the data, but
> > after some minutes of transferring the data I see the message again.
> >
> > Would you please help me in solving this problem?
> > Best Wishes,
> > Soheila
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> 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:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
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>



-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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