[FieldTrip] Bidomain model instead of dipoles
hiba fouani
hibafouani123 at hotmail.com
Fri Apr 1 12:15:53 CEST 2016
Dear fieldtripper,
I want to study source localization for ecg but with bidomain model for
sources not dipoles, is it possible with fieldtrip or openmeeg? and thank
you for suggestion for any tool.
Thank you
Hiba
> From: fieldtrip-request at science.ru.nl
> Subject: fieldtrip Digest, Vol 65, Issue 1
> To: fieldtrip at science.ru.nl
> Date: Fri, 1 Apr 2016 12:00:02 +0200
>
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> Today's Topics:
>
> 1. Question about coherence statistics (laetitia.lalla at inserm.fr)
> 2. Re: Question about coherence statistics (Snijders, T.M. (Tineke))
> 3. Re: Question about coherence statistics (laetitia.lalla at inserm.fr)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 31 Mar 2016 13:11:31 +0200
> From: laetitia.lalla at inserm.fr
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Question about coherence statistics
> Message-ID: <abb2342e7e3acc37fa03deeef989a226 at inserm.fr>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> Dear FielTrip community,
>
> Sorry to bother you again...
>
> I have a question about the statistical testing to assess coherence
> differences and the related paper by E Maris, JM Schoffelen and P Fries
> (Journal of Neuroscience Methods, 2007)
>
> I believe I am exactly in the framework described in this paper, but I
> guess there is still some crucial information that I don't understand...
>
>
> This is my story :
>
> - It's a single-subject study
>
> - I want to compare two sets of trials observed in different conditions.
>
>
> - The 2 sets of trials are exactly the same size, so my coherence
> estimate won't be biased by the "unequal sample size problem".
>
> - I just want to compare for 1 channel pair, for 1 frequency bin [6Hz
> 10Hz], so I guess the Multiple Comparison problem won't affect my
> analysis too much (either in the spatial or the spectral dimension).
>
> Based on the paper, I could refer myself to the point "2.7.1. A non
> parametric satistical test for a single signal pair and a single
> frequency bin".
>
> - Since my interest is in the coherence difference for a single signal
> pair, I can choose [|C1(f)|-|C2(f)|] as a test statistic.
>
> - And I can perform the montecarlo simulation.
>
> My question is the following : How can I implement the nonparametric
> test of the coherence difference between my 2 conditions with the
> fieldtrip functions ?
>
> This is what I did :
>
> 1) Extract and preprocess the signal from my condition 1.
>
> 2) freq1= ft_freqanalysis(cfg, signal1) (with cfg.method='mtmfft',
> cfg.output='powandcsd') ?
>
> 3) coh1= ft_connectivityanalysis(cfg, freq1)
>
> I did the same thing for the other condition ? coh2.
>
> And then for the statistics :
>
> cfg = [];
>
> cfg.statistic = 'diff'; (% because the statistic test than I chose is
> the difference [|C1(f)|-|C2(f)|])
>
> cfg.parameter='cohspctrm';
>
> cfg.method = 'montecarlo';
>
> cfg.numrandomization = 1000;
>
> cfg.ivar = 1;
>
> cfg.alpha=0.05;
>
> cfg.tail=0;
>
> cfg.correcttail='alpha';
>
> stat=ft_freqstatistics(cfg, coh1, coh2);
>
> And it gives me the following error :
>
> Error using ft_checkconfig (line 153)
>
> The field cfg.design is required.
>
> Here, I really don't understand why I'm asked for the design matrix...
> When doing the statistics for the Power, I understood that the design
> matrix was telling which trial belonged to the condition 1 and which
> trial belonged to the condition 2. But here, it doesn't make any sense
> because my coherence was calculated by averaging on the trials...
>
> Does the design matrix mean something differently here ? Or maybe I
> forgot one parameter to put in the cfg ?
>
> Any help will be appreciated !
>
> Thanks a lot for your time,
>
> Laetitia Lalla
>
> PhD student in Neurosciences
>
> INMED, Marseille, France
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 2
> Date: Thu, 31 Mar 2016 11:47:19 +0000
> From: "Snijders, T.M. (Tineke)" <tineke.snijders at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about coherence statistics
> Message-ID:
> <815A9820E75FBC4F96B7CD3A8089D11C378AE3E0 at exprd04.hosting.ru.nl>
> Content-Type: text/plain; charset="iso-2022-jp"
>
> Hi Laetitia,
>
> If you only have one subject you do need individual trial data, otherwise you can't do statistics like this.
> You need multiple observations (either subjects or trials).
>
> Best,
> Tineke
>
> ________________________________
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of laetitia.lalla at inserm.fr [laetitia.lalla at inserm.fr]
> Sent: Thursday, March 31, 2016 1:11 PM
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Question about coherence statistics
>
>
> Dear FielTrip community,
>
> Sorry to bother you again...
>
> I have a question about the statistical testing to assess coherence differences and the related paper by E Maris, JM Schoffelen and P Fries (Journal of Neuroscience Methods, 2007)
>
> I believe I am exactly in the framework described in this paper, but I guess there is still some crucial information that I don't understand...
>
>
>
> This is my story :
>
> - It's a single-subject study
>
> - I want to compare two sets of trials observed in different conditions.
>
> - The 2 sets of trials are exactly the same size, so my coherence estimate won't be biased by the ?unequal sample size problem?.
>
> - I just want to compare for 1 channel pair, for 1 frequency bin [6Hz 10Hz], so I guess the Multiple Comparison problem won't affect my analysis too much (either in the spatial or the spectral dimension).
>
>
>
> Based on the paper, I could refer myself to the point ?2.7.1. A non parametric satistical test for a single signal pair and a single frequency bin?.
>
> - Since my interest is in the coherence difference for a single signal pair, I can choose [|C1(f)|-|C2(f)|] as a test statistic.
>
> - And I can perform the montecarlo simulation.
>
>
>
> My question is the following : How can I implement the nonparametric test of the coherence difference between my 2 conditions with the fieldtrip functions ?
>
>
>
> This is what I did :
>
> 1) Extract and preprocess the signal from my condition 1.
>
> 2) freq1= ft_freqanalysis(cfg, signal1) (with cfg.method='mtmfft', cfg.output='powandcsd') ?
>
> 3) coh1= ft_connectivityanalysis(cfg, freq1)
>
>
>
> I did the same thing for the other condition ? coh2.
>
>
>
> And then for the statistics :
>
> cfg = [];
>
> cfg.statistic = 'diff'; (% because the statistic test than I chose is the difference [|C1(f)|-|C2(f)|])
>
> cfg.parameter='cohspctrm';
>
> cfg.method = 'montecarlo';
>
> cfg.numrandomization = 1000;
>
> cfg.ivar = 1;
>
> cfg.alpha=0.05;
>
> cfg.tail=0;
>
> cfg.correcttail='alpha';
>
> stat=ft_freqstatistics(cfg, coh1, coh2);
>
>
>
> And it gives me the following error :
>
> Error using ft_checkconfig (line 153)
>
> The field cfg.design is required.
>
>
>
> Here, I really don't understand why I'm asked for the design matrix... When doing the statistics for the Power, I understood that the design matrix was telling which trial belonged to the condition 1 and which trial belonged to the condition 2. But here, it doesn't make any sense because my coherence was calculated by averaging on the trials...
>
> Does the design matrix mean something differently here ? Or maybe I forgot one parameter to put in the cfg ?
>
>
>
> Any help will be appreciated !
>
>
>
> Thanks a lot for your time,
>
>
>
> Laetitia Lalla
>
> PhD student in Neurosciences
>
> INMED, Marseille, France
>
>
>
>
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160331/2a9a260f/attachment-0001.html>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 31 Mar 2016 15:22:31 +0200
> From: laetitia.lalla at inserm.fr
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about coherence statistics
> Message-ID: <e2c5530bde0e283538fc02802fadc5dc at inserm.fr>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> Dear Tineke,
>
> thank you very much for your fast answer ! I'm not sure I understand
> what you mean though... Maybe i did not express myself correctly. I do
> have individual trial data : I have 26 observations for condition 1 and
> 26 observations for condition 2.
>
> They appear :
>
> - In my structure "data" (output of ft_preprocessing) : data.trial is a
> cell {1 x nbtrials} (in my case : {1, 26})
>
> - in my structure "freq" (output of ft_freqanalysis) : freq.powspctrm is
> a matrix of dimension : nbtrials X nbchannel X nbfreq (in my case
> 26x2x25)
>
> But I don't have this information anymore in the structure "coh" (output
> of ft_connectivityanalysis) : coh.cospctrm is a matrix of dimension
> nbchannelcmb x nbfreq (in my case 1x25) since the coherence is
> calculated by averaging over trials...
>
> You may mean I should give the "freq" structures as inputs to the
> fonction ft_freqstatistics ?
>
> I just tried that : I created a structure data_all by concatenated
> data1.trial and data2.trial (and every other appropriate attribute). I
> took the Time Frequency Representation with ft_freqanalysis (with
> keeptrials='yes') to obtain a structure TFR_all (following this tutorial
> : http://www.fieldtriptoolbox.org/tutorial/natmeg/statistics This is
> actually how I did the statistics for the Power).
>
> But then, if I give this as an input to ft_freqstatistics, like this :
>
> cfg = [];
> cfg.statistic = 'diff';
> cfg.parameter='cohspctrm';
> cfg.design= [ones(1,nbtrial)) 2*ones(1, nbtrial))]; %same nb of trials
> for both condition
> cfg.method = 'montecarlo';
> cfg.numrandomization = 1000;
> cfg.ivar = 1;
> cfg.alpha=0.05;
> cfg.tail=0;
> cfg.correcttail='alpha';
> >> stat=ft_freqstatistics(cfg, FR_alltrials);
>
> I have the following error :
>
> Error using getdimord (line 15)
> field "cohspctrm" not present in data
>
> which makes a lot of sense, since I did not gave coherence as an
> input... I gave Frequency representations.. I was hoping that maybe the
> function would calculate the coherence itself for the statistics ? ^^
> But it's clearly not the way to go.
>
> Could you be a bit more explicit about what you meant ?
>
> Thanks a lot.
>
> Best,
>
> Laetitia Lalla
>
> PhD student in Neurosciences
>
> INMED, Marseille, France
>
> On 31-03-2016 13:47, Snijders, T.M. (Tineke) wrote:
>
> > Hi Laetitia,
> >
> > If you only have one subject you do need individual trial data, otherwise you can't do statistics like this.
> > You need multiple observations (either subjects or trials).
> >
> > Best,
> > Tineke
> >
> > -------------------------
> >
> > FROM: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of laetitia.lalla at inserm.fr [laetitia.lalla at inserm.fr]
> > SENT: Thursday, March 31, 2016 1:11 PM
> > TO: fieldtrip at science.ru.nl
> > SUBJECT: [FieldTrip] Question about coherence statistics
> >
> > Dear FielTrip community,
> >
> > Sorry to bother you again...
> >
> > I have a question about the statistical testing to assess coherence differences and the related paper by E Maris, JM Schoffelen and P Fries (Journal of Neuroscience Methods, 2007)
> >
> > I believe I am exactly in the framework described in this paper, but I guess there is still some crucial information that I don't understand...
> >
> > This is my story :
> >
> > - It's a single-subject study
> >
> > - I want to compare two sets of trials observed in different conditions.
> >
> > - The 2 sets of trials are exactly the same size, so my coherence estimate won't be biased by the "unequal sample size problem".
> >
> > - I just want to compare for 1 channel pair, for 1 frequency bin [6Hz 10Hz], so I guess the Multiple Comparison problem won't affect my analysis too much (either in the spatial or the spectral dimension).
> >
> > Based on the paper, I could refer myself to the point "2.7.1. A non parametric satistical test for a single signal pair and a single frequency bin".
> >
> > - Since my interest is in the coherence difference for a single signal pair, I can choose [|C1(f)|-|C2(f)|] as a test statistic.
> >
> > - And I can perform the montecarlo simulation.
> >
> > My question is the following : How can I implement the nonparametric test of the coherence difference between my 2 conditions with the fieldtrip functions ?
> >
> > This is what I did :
> >
> > 1) Extract and preprocess the signal from my condition 1.
> >
> > 2) freq1= ft_freqanalysis(cfg, signal1) (with cfg.method='mtmfft', cfg.output='powandcsd') ?
> >
> > 3) coh1= ft_connectivityanalysis(cfg, freq1)
> >
> > I did the same thing for the other condition ? coh2.
> >
> > And then for the statistics :
> >
> > cfg = [];
> >
> > cfg.statistic = 'diff'; (% because the statistic test than I chose is the difference [|C1(f)|-|C2(f)|])
> >
> > cfg.parameter='cohspctrm';
> >
> > cfg.method = 'montecarlo';
> >
> > cfg.numrandomization = 1000;
> >
> > cfg.ivar = 1;
> >
> > cfg.alpha=0.05;
> >
> > cfg.tail=0;
> >
> > cfg.correcttail='alpha';
> >
> > stat=ft_freqstatistics(cfg, coh1, coh2);
> >
> > And it gives me the following error :
> >
> > Error using ft_checkconfig (line 153)
> >
> > The field cfg.design is required.
> >
> > Here, I really don't understand why I'm asked for the design matrix... When doing the statistics for the Power, I understood that the design matrix was telling which trial belonged to the condition 1 and which trial belonged to the condition 2. But here, it doesn't make any sense because my coherence was calculated by averaging on the trials...
> >
> > Does the design matrix mean something differently here ? Or maybe I forgot one parameter to put in the cfg ?
> >
> > Any help will be appreciated !
> >
> > Thanks a lot for your time,
> >
> > Laetitia Lalla
> >
> > PhD student in Neurosciences
> >
> > INMED, Marseille, France
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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