[FieldTrip] ft_freqstatistics and FDR-correction

[Patricia Wollstadt]

Dear all,

I'm still trying to identify the underlying reason for the issue described below. I ran the analysis in debug mode (I'm using Matlab2008b and the Fieldtrip-release from the 16th of January 2011) and found that the matrix 'resample', that is generated in 'statistics_montecarlo', line 187:

resample = resampledesign(cfg, design);

doesn't contain actual permutations of my initial design, but rather sorted rowvectors from 1 to 80 (no of subjects). So (since there is no permutation of the units of observation) the 'randstat' that is subsequently calculated for each row of the resample-matrix is always the same. 
Is this maybe due to my design and my units of observations respectively? I am looking at age-dependent variations in resting-state data, so my UO are 80 subjects, divided into four age groups. The commandline-output of the 'resampledesign'-function is as follows:

total number of measurements     = 80
total number of variables        = 2
number of independent variables  = 1
number of unit variables         = 1
number of within-cell variables = 0
number of control variables      = 0
using a permutation resampling approach
repeated measurement in variable 1 over 80 levels
number of repeated measurements in each level is 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 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 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 1 1 1 1 1 


Is this correct? Shouldn't this read 'repeated measurement in variable 2 over 4 levels' with the number of subjects per group as repeated measurements within a condition? Still I am pretty sure about my design matrix, which contains the indices 1 to 80 (for all subjects) in the first row (this is my cfg.uvar) with the corresponding age groups (1 to 4) in the second row (cfg.ivar, see my previous email below). I use an 'indepsamplesF'-statistic, since I am comparing between four groups of different subjects (averaged over trials).

I hope, I got the settings and my design right. Any suggestions, whether this is a problem due to wrong configurations in my script are very welcome.

Right now I work around this issue by replacing line 279 in 'statistics_montecarlo':

tmpdesign = design(:,resample(i,:));

with: 

tmpdesign = design(:,randperm(size(design,2)));

creating permutations of my design 'by hand'. Is this acceptable or is there anything I'm maybe missing. 

Thank you very much, kind regards,

Patricia




-------- Original-Nachricht --------
> Datum: Mon, 24 Jan 2011 17:47:26 +0100
> Von: "Patricia Wollstadt" <Patricia.Wollstadt at gmx.de>
> An: fieldtrip at donders.ru.nl
> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction

> Dear Fieldtrip-users,
> 
> I'm currently trying to calculate freqstatistics for four experimental
> groups, using the following options:
> 
> groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3})
> length(subjects{4})];
> 
> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)];         
>   % 1 to N subjects
> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2))
> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership
> 
> 
> cfg=[];
> cfg.design=design;
> cfg.uvar = 1;       
> cfg.ivar = 2;    
> cfg.method = 'montecarlo';
> cfg.statistic = 'indepsamplesF';
> cfg.correctm = 'fdr';
> cfg.numrandomization = 180000;
> cfg.alpha = 0.01/7;
> cfg.tail = 1;
> cfg.design = design;
> cfg.channels = myChannels;
> cfg.avgovertime = 'yes';
> cfg.avgoverfreq = 'yes';
> cfg.frequency = [1 3];
> 
> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg);
> 
> With these settings, the coputation itself runs fine, but the resulting 
> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of
> only ones). This would mean, that I found significant effects for all
> channels. Is this possible or rather due to an error somewhere in my script? Is
> it likely, that these are 'real' zeroes or rather very small values, close
> to zero?
> Any hints and suggestions are very welcome, thank you in advance,
> 
> Kind regards
> 
> Patricia Wollstadt
> 
> 
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