[Mne_analysis] Repeated-measured oneway ANOVA / paired ttest in spatio temporal clustering

[Denis-Alexander Engemann]

Hi Laetitia,

how may 'factors' / conditions do you have?
A t-test for related samples is equivalent to a 1 smaple t-test of the
paired contrast which is the same as a repeated measures ANOVA for 2
factors after squaring the output:

def stat_fun(x):
    return mne.stats.ttest_1samp_no_p(x, sigma=1e-3, method='relative') ** 2

Also see this modified example that showd how to compute an interaction
contrast using this stat_fun.

https://gist.github.com/dengemann/ff96e48dd1dd3eeaca3e

HTH,
Denis




2014-10-27 15:03 GMT+01:00 Laetitia Grabot <laetitia.grabot at gmail.com>:

> Dear mailing list,
>
> I'm doing spatio-temporal clustering on 12 subjects in source space. Very
> basically, I would like to compare two conditions by taking into account
> subjects variability, so I need to do a paired ttest/oneway
> repeated-measure ANOVA. Yet, the spatio_temporal_cluster_test function is
> only implementing  oneway anova, while the spatio_temporal_cluster_1samp_test
> is implementing simple ttest on the difference
> *.*
> *I looked at related issues on github and found that there is a twoway
> anova with repeated measures function implemented under the name of
> f_twoway_rm but it doesn't work for oneway anova (factor_levels = [2],
> n_conditions = 2). Then I tried to build a stat_fun function from *
>
> *scipy.stats.ttest_rel:*
>
> *def stat_fun(*args):*
>
> *      a = X[0]*
> *      b = X[1]**      return *
> *scipy.stats.ttest_rel(a,b)*
>
> *But I get an error at lign 708 in _permutation_cluster_test (cannot copy
> sequence with size 2 to array axis with dimension 0), I guessed there is a
> format problem in my stat_fun function...*
>
>
> *Did someone find a way to do such an analysis?*
>
>
> *Thanks in advance,Laetitia Grabot.*
>
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