clusterrandanalysis questions

Eric Maris maris at NICI.RU.NL
Thu Aug 16 11:11:10 CEST 2007

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

MSc Cognitive Neuroscience : <>

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