[Mne_analysis] Question about permutation_cluster_test

[Dirk van Moorselaar]

Dear MNE,

Thus far I have been using Matlab scripts for my permutation tests, but I would like to use mne functionality for this as well. Today I have been playing around with some tutorials using mne.stats.permutation_cluster_test and used it on my own data as well. This seemed to work fine, however, there is one aspect that is not entirely clear to me. 

In my understanding if the argument connectivity is set to None, to be considered part of a cluster a node needs to be connected to another node in horizontal or vertical direction. But what I would like to do is to specify the connectivity matrix such that diagonals are also set to be part of the cluster. As a first attempt I tried to set connectivity with the following argument sparse.csr_matrix(np.ones((3,3))), but this gave me the error that connectivity must be of the correct size (I am comparing 3d arrays with the following dimensions: 16 x 19 x 141, where the first dimension are the number of observations)

Could you please tell me how to set the connectivity matrix to accomplish this or could you point me to a tutorial where this is explained.

Thanks in advance,

Dirk



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