[Mne_analysis] plot_cluster_stats_spatio_temporal

[Eric Larson]

Hey Matt,

The statistical functions are designed to accommodate different statistical
measures on their inputs. See if you can use the 2-sample version, changing
the statistical function (`stat_fun`) being called to one of your own (by
default it uses `f_oneway`):

https://github.com/mne-tools/mne-python/blob/master/mne/stats/cluster_level.py#L1267

Sorry this function isn't in the documentation -- it should be! I fixed it
in master, so the function should show up in the developmental version of
the documentation in the next couple days:

http://martinos.org/mne/dev/python_reference.html#statistics

In the meantime you can see the example using it in the docs:

http://martinos.org/mne/stable/auto_examples/stats/plot_cluster_stats_spatio_temporal_2samp.html#example-stats-plot-cluster-stats-spatio-temporal-2samp-py

If this function won't work for your use case, open an issue on GitHub and
we can talk about how to expand or modify the API (and hopefully add an
example along the way).

Cheers,
Eric



On Wed, Jan 8, 2014 at 11:23 AM, Matt Erhart <merhart at ucsd.edu> wrote:

> Is there a way currently to do the 1samp test without assuming equal
> variance?
>
>
> On Wed, Jan 8, 2014 at 12:27 AM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
>
>> > In the example online, plot_cluster_stats_spatio_temporal.py, X is
>> passed in
>> > to ttest 0 and 1 in the forth dimension: X = X[:, :, :, 0] - X[:, :, :,
>> 1] #
>> > make paired contrast.
>> > That subtraction seems strange to me since it seems to lose the variance
>> > unique to each condition. I would have expected something more like
>> > ...1samp_test(X[:, :, :, 0], X[:, :, :, 1]). What am I missing here?
>>
>> you're right. We assume here equal variance and then the paired t test
>> is just a one sample test on the difference.
>>
>> suggestions of improvement are really welcome.
>>
>> > Also, my ultimate goal is 1samp and 2samp spatio-temporal clustering
>> with
>> > TFCE with MEG. ANOVA for groupxcondition would be great as well. In
>> > spatio_temporal_cluster_1samp_test, the doc says TFCE will be used if a
>> dict
>> > is passed in for threshold=, but what is that dict suppose to look like?
>>
>> have a look at the TFCE example
>>
>>
>> http://martinos.org/mne/stable/auto_examples/stats/plot_cluster_methods_tutorial.html
>>
>> and especially the variable:
>>
>> threshold_tfce
>>
>> > Much thanks for the excellent package,
>>
>> thanks
>>
>> > P.S. Anaconda was really important for getting this working in centos5
>> > without root access. Spyder is working as well which is great for
>> > transitioning from matlab.
>>
>> that's indeed what we recommend to install to get started
>>
>> Best,
>> Alex
>>
>
>
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