Statistical comparisons in virtual electrode spectrograms

[Eric Maris]

Hi Piers,


> I would like to try: "a neighbourhood structure as a cell array (in your
> case, of length 1) of structs". But could you clarify a little more what
> the syntax would be for this cfg?

Type "Help clusterrandanalysis" on the Matlab command line.

> Re- the hypothesis tests, when I put the script together I hadn't really
> thought through the hypothesis testing carefully. I was just trying to
> get something to work at all.
>
> But you are quite right, it doesn't make sense to statistically compare
> E versus E+I
>
> However, I do want to apply a test, separately, for E baseline v E
> active, *and* E+I baseline versus E+I active.
>
> Might it make sense, do you think, to compare ([E+I]-E) baseline versus
> ([E+I]-E) active, to try to work out whether there is indeed any
> significant induced activity?


I think this makes sense. For activation-versus-baseline testing, you better
use the activation-versus-baseline t-statistic instead of the
dependent-samples t-statistic.


Greetings,

Eric



>
> Best regards
>
> Piers
> > Hi Piers,
> >
> >
> >
> > In my first reply to your email, I didn't notice that you were analyzing
> > virtual channels. In that case, the suggestion in my previous email will
not
> > work. As I see it now, you have only a single virtual channel. In other
> > words, you do not have a spatial dimension in your data. Nevertheless,
> > clusterrandanalysis wants a spatial neighbourhood structure. In the case
of
> > virtual channels, you have to construct this neighbourhood structure by
> > hand. Read the help info of clusterrandanalysis, and you will find out
how
> > to specify a neighbourhood structure as a cell array (in your case, of
> > length 1) of structs.
> >
> > I also read that you want to compare evoked and (evoked + induced) power
> > spectra. Are these power spectra calculated on the same raw data? If
this is
> > the case, does it make sense to test the null hypothesis that they come
from
> > the same probability distribution (which is what clusterrandanalysis
tests)?
> > This null hypothesis would imply that the pure induced power spectra are
> > zero. Do I see this correctly?
> >
> >
> > Greetings,
> >
> > Eric
> >
> >
> >
> >
> >> -----Original Message-----
> >> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> >>
> > Behalf Of
> >
> >> Piers Cornelissen
> >> Sent: Wednesday, November 08, 2006 3:19 PM
> >> To: FIELDTRIP at NIC.SURFNET.NL
> >> Subject: [FIELDTRIP] Statistical comparisons in virtual electrode
> >>
> > spectrograms
> >
> >> Dear all
> >>
> >> Can anyone advise on the following:
> >>
> >> I have 6 sets of virtual electrode data (from CTF based MEG recordings)
> >> from a total of 9 subjects, each of whom carried out 4 conditions of
> >> interest.
> >>
> >> So far, for each virtual electrode I have succeeded (I hope) in
computing
> >> group level spectrograms for each condition, where each spectrogram
> >> reflects either evoked or evoked+induced power changes.
> >>
> >> What I would like to do is to a) compare spectrograms, and also
b)compute
> >> statistics for each group level spectrogram to ask the question whether
> >> the power changes in the active window (0 - 700ms) are significantly
> >> different from the those in the passive/baseline window (-250 - 0 ms).
> >>
> >> So far I have had alot of help from Jan, and, on his suggestion, I have
> >> copied out my query below, plus provided the matlab scripts which cause
> >> the problem:
> >>
> >> The attached script E_versus_EI.m shows the code for
> >> analysing one condition from one particular virtual electrode. This
gives
> >> the evoked as well as the evoked+induced spectrograms (as far as I
> >> understand it).
> >>
> >> To carry out the comaprison between the evoked versus evoked+Induced
test,
> >> I thought I should be able to modify the freqgrandaverage step for
> >> generating both iefgranfavg and efgrandavg by setting
cfg.keepindividual
> >> to 'yes'. In doing so, I was hoping that this would retain the 9
separate
> >> powerspectra in each case, which it seems to have done. I was then
hoping
> >> that this would be sufficient input to the second script
test_clusrand.m
> >> (which is just a minor modification of  E_versus_EL.m). Certainly the
> >> powspctrm field for each dataset appears as: [4-D double] which I think
is
> >> correct.
> >>
> >> However, when I ran clusterrandanalysis on iefgranfavg and efgrandavg,
I
> >> got the following errors:
> >>
> >>
> >> cfg15 =
> >>
> >>          statistic: 'depsamplesT'
> >>        alphathresh: 0.0500
> >>       makeclusters: 'yes'
> >>          minnbchan: 2
> >>    clusterteststat: 'maxsum'
> >>             onetwo: 'twosided'
> >>              alpha: 0.0500
> >>         nranddraws: 100
> >>            channel: {'V0'}
> >>
> >>
> >>>> %cfg15.latency = [0 0.5]  % increases sensitivity if prior temporal
> >>>>
> >> information is  knowm
> >>
> >>>> cfg15.frequency = [5 40];
> >>>>
> >>>> %frange = 'all_freqs';  % file addition for saving
> >>>>
> >>>> [clusrand] = clusterrandanalysis (cfg15, ind_efgrandavg,
> >>>>
> >> ind_iefgrandavg);
> >> Selecting and formatting the data.
> >> selected 1 channels
> >> selected 191 time bins
> >> selected 176 frequency bins
> >> Calculating the neighbourhood structure of the channels.
> >> ??? Error using ==> clusterrandanalysis (getneighbgeometry)
> >> Did not find gradiometer or electrode information.
> >>
> >> Error in ==> /home/willis/plc/matlab/clusterrandanalysis.m
> >> On line 473  ==> [cfg,data] = getneighbgeometry(cfg,data,varargin{1});
> >>
> >>
> >> I noticed also that the way I used freqgrandaverage in order to compile
> >> the two datasets appeared to throw out the gradiometer information. At
> >> least there was a warning to this effect. So, I am guessing that using
> >> freqgrandaverage in this way is incorrect. Therefore please could
anyone
> >> suggest how I compile my 2 sets of nine spectrograms in such a way that
> >> they provide appropriate input to clusterrandanalysis. Or, if as Jan
seems
> >> to suggest, that clusterrandanalysis can't cope with virtual electrode
> >> data, does anyone have any other clever solutions.
> >>
> >> Please!
> >>
> >> Thanks in anticipation
> >>
> >> Piers C
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> >