[FieldTrip] fieldtrip Digest, Vol 41, Issue 16

Tue Apr 8 15:38:38 CEST 2014

Hi Marlene, The fix was implemented yesterday, so Sunday's version unfortunately does not contain it. It seems there is currently a problem with the ftp file, so please try again as soon as you can download the latest version. If the problem still exists, please file a bug at http://bugzilla.fcdonders.nl/ and we'll try to replicate your issue. Best, Arjen ----- Oorspronkelijk bericht -----
> Van: "Marlene Bönstrup" <marlene.boenstrup at googlemail.com>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Dinsdag 8 april 2014 13:31:25
> Onderwerp: Re: [FieldTrip] fieldtrip Digest, Vol 41, Issue 16
> 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 > :
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
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> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> > 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
> > -------------- next part --------------
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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.
> > ------------------------------
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > End of fieldtrip Digest, Vol 41, Issue 16
> > *****************************************
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
-- Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Email: a.stolk at donders.ru.nl Phone: +31(0)243 68294 Web: www.arjenstolk.nl
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