[FieldTrip] ft_freqstatistics and FDR-correction

Michael Wibral michael.wibral at web.de
Tue Feb 1 18:29:57 CET 2011


Hi Patricia,

it seems that things are clarified now. I just do not know what was actually wrong with your code  Was it the superfluous specification of  cfg.uvar??
Could you let us know? Thanks.

Michael
-----Urspr√ľngliche Nachricht-----
Von: "Patricia Wollstadt" <Patricia.Wollstadt at gmx.de>
Gesendet: Feb 1, 2011 4:34:04 PM
An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction

>Hi Michael, Hi Jan-Mathijs,
>
>thank you very much for the advice/clarification. Everything seems to run fine now (with the corrected design).
>
>Thank you very much,
>
>Best
>
>Patricia
>
>
>-------- Original-Nachricht --------
>> Datum: Wed, 26 Jan 2011 10:08:51 +0100 (CET)
>> Von: "Michael Wibral" <michael.wibral at web.de>
>> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
>> Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction
>
>> Hi Patricia,
>> 
>> I also would have thought your design to be correct. Maybe the
>> unneccessary specification of the uvar screws thinsg up??
>> 
>> However, you really do not have any repeated measures in your design -
>> here the output of FT is correct. I interpret it in the following way: You
>> specified cfg.uvar - indicating to FT the possibility that this might be a
>> repeated measures design. FT identified the units of observation as being 80
>> (correct), and then checked how many repeated measures you ran in each UO
>> and found just 1 - which is also correct. I agree that naming the units of
>> observation (UO) as 'levels' of the UO variable is a bit odd, should rather
>> be 'units of observation'. 
>> 
>> The concept of repeated measures is also very often misunderstood: in
>> repated measures you do not actually repeat anything, rather you perform
>> different measurements (treatments) WITHIN a unit of observation - so a repated
>> measures design is a within UO design. Your subjects just have one age, so
>> there are no different treatments (levels of the indep variable) per
>> subjects and, hence, no 'repeated measures'.
>> 
>> Hope this clarifies terminology for further discussion.
>> 
>> Michael
>> 
>> 
>> -----Urspr√ľngliche Nachricht-----
>> Von: "jan-mathijs schoffelen" <jan.schoffelen at donders.ru.nl>
>> Gesendet: Jan 25, 2011 8:57:03 PM
>> An: "Email discussion list for the FieldTrip project"
>> <fieldtrip at donders.ru.nl>
>> Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction
>> 
>> >Hi Patricia,
>> >
>> >I don't really understand what is going on, but could you try to  
>> >specify your design only in a single row (design = design(2,:) in your  
>> >case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how  
>> >it runs? As such the uvar row is not relevant in an independent  
>> >samples design.
>> >
>> >Best,
>> >
>> >Jan-Mathijs
>> >
>> >
>> >
>> >On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote:
>> >
>> >> 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" 
>> >>> 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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>> >>
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>> >> _______________________________________________
>> >> fieldtrip mailing list
>> >> fieldtrip at donders.ru.nl
>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >
>> >Dr. J.M. (Jan-Mathijs) Schoffelen
>> >Donders Institute for Brain, Cognition and Behaviour,
>> >Centre for Cognitive Neuroimaging,
>> >Radboud University Nijmegen, The Netherlands
>> >J.Schoffelen at donders.ru.nl
>> >Telephone: 0031-24-3614793
>> >
>> >_______________________________________________
>> >fieldtrip mailing list
>> >fieldtrip at donders.ru.nl
>> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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