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

[Denis A. Engemann]

Hi,



> On 27 Oct 2014, at 15:57, Laetitia Grabot <laetitia.grabot at gmail.com> wrote:
> 
> Ok so I understood that paired ttest = ttest of the paired contrast. Yet I didn't see why a paired ttest is the same thing as a 2 factors repeated measures anova.

it's more precisely a 1 factot repeated measures analysis with 2 factor levels. the example shows how to use. this for a 2 x 2 analysis

> I would understand the equivalence between a paired ttest and a one way repeated measures anova, but why 2 factors? I also don't understand the squared output...

the f-dist can be obtained from squaring the t-dist. you can try it and / or google it. a 1-sided t-dist is obtained from computing the square root of the f-dist. this is only valid for 1 factor with 2 levels

> And I have only one factor "Condition" with two levels "condition 1" and "condition 2". 
> 
> 2014-10-27 15:20 GMT+01:00 Denis-Alexander Engemann <denis.engemann at gmail.com>:
>> 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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