[FieldTrip] Question about coherence statistics
laetitia.lalla at inserm.fr
laetitia.lalla at inserm.fr
Thu Mar 31 15:22:31 CEST 2016
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
>
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