[FieldTrip] ft_freqstatistics and FDR-correction

Rodolphe Nenert batrod at gmail.com
Tue Feb 1 18:38:26 CET 2011 

Dear Patricia and others that participated to this discussion.

I had recently the same problem, using ft_freqstatistics with Montecarlo to
correlate Time-frequency power values and behavioral results.
All my p-values were first found to be 0, resulting in a mask full of 1.
By removing the useless cfg.uvar, the script made the correct analysis and
reported good correlation values.

Hope this helps,

Rodolphe.

On Tue, Feb 1, 2011 at 11:29 AM, Michael Wibral <michael.wibral at web.de>wrote:

> 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
> -----Ursprüngliche 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
> >>
> >>
> >> -----Ursprüngliche 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
> >> >
> >> >_______________________________________________
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> >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
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