[FieldTrip] denoising data
Haiteng Jiang
haiteng.jiang at gmail.com
Tue Apr 8 15:15:01 CEST 2014
Hi Ana& Sara,
denoise_synthetic use linear regression to regress the noise
out . The parameters are set by the manufacture company technicians
while denoise_pca is a data- driven method by removing reference channels
background noise. In principle , either is fine. Personally, I prefer to
only use denoise_synthetic. You don't need to denoise twice and you do
the component analysis later anyway.
Best,
Haiteng
On 8 April 2014 12:00, <fieldtrip-request at science.ru.nl> wrote:
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> Today's Topics:
>
> 1. Re: denoising data (Todorovic, A.)
> 2. surfaceplot made by ft_sourceplot sparing the frontal lobes
> (Marlene B?nstrup)
> 3. Re: surfaceplot made by ft_sourceplot sparing the frontal
> lobes (Arjen Stolk)
> 4. fieldtrip2eeglab (Tyler Grummett)
> 5. fieldtrip2eeglab (Julian Keil)
> 6. Re: denoising data (s.rombetto at cib.na.cnr.it)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 8 Apr 2014 07:25:18 +0200 (CEST)
> From: "Todorovic, A." <a.todorovic at fcdonders.ru.nl>
> To: FieldTrip List <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] denoising data
> Message-ID:
> <
> 818248357.305942.1396934718615.JavaMail.root at monoceros.zimbra.ru.nl>
> Content-Type: text/plain; charset=utf-8
>
> Hi Haiteng,
>
> Thanks for your reply.
>
> Just to be sure if I understand you correctly - do you use BOTH
> denoise_pca and denoise_synthetic on the same data?
>
> If not, how do you choose which one to use?
>
> Cheers,
> Ana
>
> >
> > Dear Ana,
> >
> >
> > If I understand correctly , we use ft_denoise_synthetic and
> > ft_denoise_pca to reduce noise due to recording (e.g. environment
> noise ,
> > thermal noise... ) not the brain signal artefact (e.g eye blink).
> Normally
> > ,I use these two functions in the very early stage .
> >
> > Best,
> > Haiteng
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 8 Apr 2014 09:07:46 +0200
> From: Marlene B?nstrup <marlene.boenstrup at googlemail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] surfaceplot made by ft_sourceplot sparing the
> frontal lobes
> Message-ID:
> <CAG0LeN=
> hQuwNwyu2qf-GFmF84qzVje7ENjq86MSsrpE31_J2vQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear fieldtrip-experts,
>
> The plot I generated by ft_sourceplot using cfg.method = 'surface' with
> either projectionemthod 'nearest' or 'project' looks funny. The frontal
> lobes don't show any activation, they are just left grey. And also specific
> activations on the cortex are shifted towards the back (y-axis). I compared
> the same 3-D- sourceactivation data (interpolated on the standard T1 output
> of ft_interpolate with ft_interpolate) in an orthoplot and there the
> sourceactivation is neatly arranged in the whole brain volume, including
> the frontal lobes. So that the mistake must origin in the ft_sourceplot
> function.
> I use the version of the 18th of December 2013.
>
> Do you know this problem and can help me with it?
> If not, do you have an idea to solve it or cirumvent it?
>
> Thanks in advance,
> Marlene
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>
> Message: 3
> Date: Tue, 8 Apr 2014 10:59:00 +0200
> From: Arjen Stolk <a.stolk8 at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] surfaceplot made by ft_sourceplot sparing the
> frontal lobes
> Message-ID:
> <CAAiwptRCAm4xwLyyLAK4gAgP-B4A1QyLzanOyUkAay=
> nRhoRBQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Marlene,
>
> Could you download today's version of FieldTrip, and let us know whether
> this problem still occurs? I'm saying because we just made an update to
> surface plotting, potentially solving your issue.
>
> Best,
> Arjen
>
>
> 2014-04-08 9:07 GMT+02:00 Marlene B?nstrup <
> marlene.boenstrup at googlemail.com
> >:
>
> > Dear fieldtrip-experts,
> >
> > The plot I generated by ft_sourceplot using cfg.method = 'surface' with
> > either projectionemthod 'nearest' or 'project' looks funny. The frontal
> > lobes don't show any activation, they are just left grey. And also
> specific
> > activations on the cortex are shifted towards the back (y-axis). I
> compared
> > the same 3-D- sourceactivation data (interpolated on the standard T1
> output
> > of ft_interpolate with ft_interpolate) in an orthoplot and there the
> > sourceactivation is neatly arranged in the whole brain volume, including
> > the frontal lobes. So that the mistake must origin in the ft_sourceplot
> > function.
> > I use the version of the 18th of December 2013.
> >
> > Do you know this problem and can help me with it?
> > If not, do you have an idea to solve it or cirumvent it?
> >
> > Thanks in advance,
> > Marlene
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
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> ------------------------------
>
> Message: 4
> Date: Tue, 8 Apr 2014 09:01:47 +0000
> From: Tyler Grummett <tyler.grummett at flinders.edu.au>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] fieldtrip2eeglab
> Message-ID:
> <
> 36a06a30eef54304859a734a2deb7153 at SIXPR03MB368.apcprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> ?Hey fieldtrip,
>
>
> Is there a fieldtrip2eeglab function somewhere?
>
>
> It says in the documentation of 'integrating with eeglab', and I was
> wondering whether there already was one.
>
>
> Tyler
>
>
> *************************
>
> Tyler Grummett ( BBSc, BSc(Hons I))
> PhD Candidate
> Brain Signals Laboratory
> Flinders University
> Rm 5A301
> Ext 66124
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> ------------------------------
>
> Message: 5
> Date: Tue, 8 Apr 2014 11:19:34 +0200
> From: Julian Keil <julian.keil at gmail.com>
> To: Tyler Grummett <tyler.grummett at flinders.edu.au>, FieldTrip
> discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] fieldtrip2eeglab
> Message-ID: <60EC99B5-A742-420D-84A2-3B86336EB37A at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Tyler,
>
> there was a mail by Arno Delorme last year containing the function.
>
> See below.
>
> Best,
>
> Julian
> ********************
> Dr. Julian Keil
>
> AG Multisensorische Integration
> Psychiatrische Universit?tsklinik
> der Charit? im St. Hedwig-Krankenhaus
> Gro?e Hamburger Stra?e 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax: +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Anfang der weitergeleiteten E-Mail:
>
> > Von: Arnaud Delorme <arno at cerco.ups-tlse.fr>
> > Betreff: Re: [FieldTrip] Channel layout FT to EEGLAB
> > Datum: 29. Oktober 2013 01:27:53 MEZ
> > An: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Antwort an: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >
> > Dear Rajat,
> >
> > this old function transforms EEG data contained in the Fieldtrip
> structure into an EEGLAB structure.
> > After you have done that, to transform a channel location file, simply
> type in
> >
> > EEG.chanlocs = struct('labels', cfg.elec.label, 'X',
> mattocell(cfg.elec.pnt(1,:)), 'Y', mattocell(cfg.elec.pnt(2,:)),'Z',
> mattocell(cfg.elec.pnt(3,:)));
> > EEG.chanlocs = convertlocs(EEG.chanlocs, 'cart2all');
> >
> > This code is untested. You might have to switch X, Y and Z to obtain the
> correct orientation for the electrode cap.
> > Best,
> >
> > Arno
> >
> >
> >
> > On Oct 28, 2013, at 7:36 AM, Raquel Bibi <bibi.raquel at gmail.com> wrote:
> >
> >> Hi Rajat,
> >> I don't know EEGLAB, but I use the "ordered" option in Fieldtrip to
> display my time-locked ICA components.
> >>
> >> Best,
> >>
> >> Raquel
> >>
> >>
> >> On Mon, Oct 28, 2013 at 9:39 AM, Rajat Thomas <rajatthomas at gmail.com>
> wrote:
> >> Dear all,
> >>
> >> I made a layout file using the image of the ecog array I had, just like
> described in the
> >> tutorial.
> >>
> >> I would like to port this to EEGLAB, so that I can use the various ICA
> options to plot
> >> the components at the channel locations and so on.
> >>
> >> Could anyone either point me to a file that does this conversion? or
> >> Any way of using ICA within fieldtrip to plot the various components on
> the different
> >> channels using the layout file?
> >>
> >> I know it is used for channel rejection and so on but any help on
> plotting the components
> >> back on the ICA would be appreciated.
> >>
> >> Thanks a lot in advance.
> >>
> >> Rajat
> >>
> >> --
> >> Rajat Mani Thomas
> >> Netherlands Institute for Neuroscience
> >> Amsterdam, The Netherlands
> >> http://www.cita.utoronto.ca/~thomas
> >>
> >> _______________________________________________
> >> 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
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> > _______________________________________________
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> ------------------------------
>
> Message: 6
> Date: Tue, 8 Apr 2014 11:51:12 +0200
> From: s.rombetto at cib.na.cnr.it
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] denoising data
> Message-ID: <20140408115112.cn1ddeuo840s8s84 at arco.cib.na.cnr.it>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Hi
> I am interested in this topic too.
> As I have mainly environmental noise I use denoise_pca but I would
> like to understand if with a different code I couold improve my S/N
> ratio. Moreover I would ask if there is any difference if you apply
> first one denoising procedure or the other.
>
> Regards
> Sara Rombetto, PhD
>
> > Hi Haiteng,
> >
> > Thanks for your reply.
> >
> > Just to be sure if I understand you correctly - do you use BOTH
> > denoise_pca and denoise_synthetic on the same data?
> >
> > If not, how do you choose which one to use?
> >
> > Cheers,
> > Ana
> >
> >>
> >> Dear Ana,
> >>
> >>
> >> If I understand correctly , we use ft_denoise_synthetic and
> >> ft_denoise_pca to reduce noise due to recording (e.g. environment
> noise ,
> >> thermal noise... ) not the brain signal artefact (e.g eye blink).
> Normally
> >> ,I use these two functions in the very early stage .
> >>
> >> Best,
> >> Haiteng
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> -------------------------
> Dott.ssa Sara Rombetto
> Istituto di Cibernetica
> "E. Caianiello"
> Via Campi Flegrei, 34
> 80078 Pozzuoli (NA)
> Italy
> mob +39 3401689815
> tel +39 0818675361
> fax +39 0818675128
> Lab MEG 0817483511
> --------------------------
> "I disapprove of what you say, but I will defend to the death your
> right to say
> it." [Evelyn Beatrice Hall, The Friends Of Voltaire]
>
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> End of fieldtrip Digest, Vol 41, Issue 16
> *****************************************
>
--
Haiteng Jiang
PhD candidate
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Visiting address
Room 2.32
Donders Centre for Cognitive Neuroimaging
Kapittelweg 29
6525 EN Nijmegen
the Netherlands
Tel.: +31 (0)243668291
Web: https://sites.google.com/site/haitengjiang/
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