clusterrandanalysis questions

[Sameer Walawalkar]

Thanks Eric for your email,

Given below is the info you have asked.

best,
sameer

cfg = [];
     cfg.channelcmb = ['MEG1833' 'MEG'];
     cfg.statistic = 'indepsamplesZcoh' ;
     cfg.alphathres = 0.05 ;
     cfg.alpha = 0.05 ;
     cfg.clusterteststat = 'maxsum' ;
     cfg.onetwo = 'onesided_1<2' ;
     cfg.makeclusters = 'yes' ;
     cfg.minnbchan  = 2;
     cfg.nranddraws = 500;

     [clusrand] = clusterrandanalysis(cfg, CSD1 , CSD2);



screen O/P

Selecting and formatting the data.
selected 511 channelcombinations
selected 1 time bins
selected 13 frequency bins
Calculating the neighbourhood structure of the channels.
Obtaining the gradiometer configuration from the first dataset.
Running the statistics engine.
Statistic-specific preprocessing (calculating critical values,
initializing draws from the randomization distribution, ...).
randomization 0 500
.
.
.
randomization 499 500
randomization 500 500

clusrand =

                       stats: [205x13 double]
                   raweffect: [205x13 double]
                   obsmeanc1: [205x13 double]
                   obsmeanc2: [205x13 double]
                 posclusters: [1x7 struct]
                 negclusters: []
         posclusterslabelmat: [205x13 double]
         negclusterslabelmat: []
                    critvals: 204.1906
                    labelcmb: {205x2 cell}
                        freq: [6 8 10 12 14 16 18 20 22 24 26 28 30]
                        time: NaN
                         cfg: [1x1 struct]













On Thu, 16 Aug 2007, Eric Maris wrote:

> Dear Sameer,
>
>
>
>
>
>> 1)   cfg.onetwo = 'onesided_2<1'  vs  cfg.onetwo = 'onesided_1<2
>
>>> From my understanding, it seems that one sided tests only look for
>
>> positive clusters i.e. the test statistic higher than cfg.alphathresh.
>
>> Thus clusters showing up as posclusters for coherence difference in one
>
>> case should not show up at all in the other. Yet, both the tests seem to
>
>> give me same clusters.
>
>
>
> If this is the case, then there is an error in the code. Can you send me
> your config and screen output of clusterrandanalysis?
>
>
>
>>
>
>> 2)   using cfg.onetwo = twosided I should get clusters which in some
>
>> way are union of the two sets above. Yet, I seem to get completely
>
>> different clusters, sometimes with  nothing in common between twosided and
>
>> onsesided tests.
>
>
>
> The clusters with the twosided-option should NOT be the union of the
> clusters with the two onesided options. This is because the thresholding
> values with the twosided-option are at cfg.alphathresh/2 and
> (1-cfg.alphathresh/2), whereas for the two onesided options they should be
> at, respectively, cfg.alphathresh and (1-cfg.alphathresh).
>
>
>
>
>
>> 3)   Most clusters I find seem to have a high p-value. Would the
>
>> confidence increase if I use a different alphathresh which I think is used
>
>> for thresholding the Z-statistic for defining clusters. (I just realized
>
>> that I neglected to define cfg.alphathresh and though I could not find a
>
>> default value used in clusterandanalysis, the program is obviously using
>
>> some).
>
>
>
> On the basis of my experience, I do not expect a substantial influence of
> the cfg.alphathresh value on the p-values.
>
>
>
>> 4)   What is the motivation behind  cfg.minnbchan ? Should it be based
>
>> upon the neurobiological effect I am investigating?
>
>
>
> The motivation behind cfg.minnbchan is that some samples (i.e.,
> channel-frequency-pairs or channel-frequency-time-triplets) with a big
> sample-specific statistic may have a few neighbouring samples with also a
> big sample-specific statistic, just by chance. To "prune out" these chance
> connections, set cfg.minnbchan high (e.g., 3).
>
>
>
>
>
> Kind regards,
>
>
>
> Eric Maris
>
>
>
>
>
>
>
>
>
> dr. Eric Maris
>
> NICI/Biological Psychology and
>
> F.C. Donders Center for Cognitive NeuroImaging
>
> University of Nijmegen
>
> P.O. Box 9104
>
> 6500 HE Nijmegen
>
> The Netherlands
>
> T:+31 24 3612651 (NICI)
>
> T:+31 24 3610754 (FCDC)
>
> F:+31 24 3616066 (NICI)
>
> E: maris at nici.ru.nl
>
> MSc Cognitive Neuroscience : <http://www.ru.nl/master/cns/>
> www.ru.nl/master/cns/
>
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.