[FieldTrip] Pb with ft_freqstatistics when averaged over channels : NaNs

[laetitia.lalla at inserm.fr]

Hello again, 

I actually solved my problem... It was pretty silly... 

I needed to put 1 and 2 in my design matrix instead of 0 and 1... 

It's in the code here : 

in ft_statfun_indepsamplesT.m 

row 77 

% perform some checks on the design
sel1 = find(design(cfg.ivar,:)==1);
sel2 = find(design(cfg.ivar,:)==2); 

Sorry about that... But maybe it can help other people ? 

Have a nice day, 

Laetitia 

On 29-03-2016 10:50, laetitia.lalla at inserm.fr wrote: 

> Dear FieldTrip community, 
> 
> I have a similar problem that may be of help here. 
> 
> It's my first message on this mailing list so, first of all, thank you very much for this free toolbox and the help you're providing. I'm a PhD student in Marseille (France) and I'm doing LFP recordings with tetrodes or silicon probes in freely moving rats. (I apologize in advance for this very detailed - and long - email). 
> 
> I'm trying to compare the power in a certain frequency range between 2 conditions (Trial and Baseline). I can see a clear rising during the trial and I want to run the statistics now. 
> 
> Like Zita, I'd like to run a cluster permutation test on data with frequency and time information, and my signal is averaged over channels. 
> 
> I followed this tutorial : http://www.fieldtriptoolbox.org/tutorial/natmeg/statistics. [1]Based on this, this is what I did : 
> 
> 1) I cut epochs of 6s (trials), filter [0.1 250Hz] and average over channels to have an averaged signal per probe (32 channels = 4 shanks = 1 probe). 
> 
> 2) I do the same for the baseline. 
> 
> 3) I create a structure data_all which gather all the epochs, with the appropriate design matrix (0 if baseline, 1 if trial). 
> 
> 4) I do a Time Frequency Transform averaged over time with ft_freqanalysis, 'mtmfft', with keeptrials='yes'. It give me, for each trial, a profile Power=f(Freq) averaged during the time of the epoch. The difference in my frequency range is very clear when I plot the profiles. 
> 
> 5) I use ft_freqstatistics like this : 
> 
> cfg = []; 
> 
> cfg.channel = 'Str'; 
> 
> cfg.design = data_all.designmatrix; 
> 
> cfg.method = 'montecarlo'; 
> 
> cfg.numrandomization = 500; 
> 
> cfg.statistic = 'indepsamplesT'; 
> 
> cfg.ivar = 1; 
> 
> cfg.correctm = 'cluster'; 
> 
> cfg.neighbours = []; 
> 
> cfg.alpha=0.05; 
> 
> cfg.tail=0; 
> 
> cfg.correcttail='alpha'; 
> 
> [stat]=ft_freqstatistics(cfg, FR_alltrials) 
> 
> And this is not working because I have only NaNs... 
> 
> stat = 
> 
> stat: [NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN] 
> 
> prob: [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1] 
> 
> cirange: [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0] 
> 
> mask: [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0] 
> 
> ref: [NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN] 
> 
> dimord: 'chan_freq' 
> 
> freq: [1x25 double] 
> 
> label: {'Str'} 
> 
> cfg: [1x1 struct] 
> 
> Would you have an idea to resolve my problem ? Maybe I forgot to precise a parameter somewhere ? 
> 
> Thank you for your help! 
> 
> Best regards, 
> 
> Laetitia 
> 
> On 24-03-2016 13:15, Zita Eva Patai wrote: 
> 
>> Dear FT-ers 
>> 
>> I would like to run a cluster permutation test on data where i have frequency and time information, but have averaged over channels. 
>> 
>> I am setting my cfg for ft_freqstatistics as usual, but asking for all times and channels (no averaging). I am also not setting the cfg.neighbours option, because there aren't any. In this case it won't run and asks for that setting. If I then set cfg.neighbour = []; then it complains it cannot find the .powspctrm of my data.  
>> 
>> If I do not ask for cluster correction, it runs through fine and I get a stat structure out of it, but this is uncorrected.  
>> 
>> Is there an easy way to fix this? 
>> 
>> I am using the FT inside SPM12. 
>> 
>> Thanks very much, 
>> zita 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

  

Links:
------
[1] http://www.fieldtriptoolbox.org/tutorial/natmeg/statistics
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