[FieldTrip] fieldtrip Digest, Vol 41, Issue 16
Marlene Bönstrup
marlene.boenstrup at googlemail.com
Tue Apr 8 13:31:25 CEST 2014
Dear Arjen,
thanks for your quick reply.
With the version of sunday (yesterdays version the file was invalid, my
windows couldn't open it and there is not yet a version of today) the
misplotting still occurs.
I dont know if attachments work in this email list, but attached there is
the surface and the orthoplot of exactly the same interploated data.
2014-04-08 12:00 GMT+02:00 <fieldtrip-request at science.ru.nl>:
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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
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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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]
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
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> End of fieldtrip Digest, Vol 41, Issue 16
> *****************************************
>
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