[FieldTrip] A question

Stephen Whitmarsh stephen.whitmarsh at gmail.com
Thu Feb 16 12:39:25 CET 2012


Dear All,

All true, except that ICA implemented by FT does demean the data
before unmixing by default. Use cfg.demean = 'no' if you don't want
to.

cheers,
stephen

On 16 February 2012 12:35, Stephen Politzer-Ahles
<politzerahless at gmail.com> wrote:
> 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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>> End of fieldtrip Digest, Vol 15, Issue 17
>> *****************************************
>
>
>
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




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