[Mne_analysis] using find_ch_connectivity for spatio-temporal clustering

[Denis A. Engemann]

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Hi Dillan,

if you do not untuple the output of the function like this:

connect_matrix, names = mne.channels.find_ch_connectivity(epochs.info,ch_type='eeg’)

you should pass

connect_matrix[0]

into the  clustering permutation function.

Check here for the function signature:
https://www.martinos.org/mne/stable/generated/mne.channels.read_ch_connectivity.html#mne.channels.read_ch_connectivity

Hope that helps,

Denis

> On Jul 31, 2019, at 11:03 PM, Dillan Cellier <cellierdillan at gmail.com> wrote:
> 
>         External Email - Use Caution        
> 
> 
> Hello MNE users,
> 
> I am attempting to use the function mne.channels.find_ch_connectivity() to generate a matrix of the channel connectivity. I'd like to use this matrix as an input to mne.stats.spatio_temporal_cluster_1samp_test() for the 'connectivity' argument. 
> 
> I am getting an error when I feed the output of find_ch_connectivity into spatio_temporal_cluster_1samp_test. 
> 
> Here is my code:
> 
> connect_matrix=mne.channels.find_ch_connectivity(epochs.info,ch_type='eeg')
> 
> 
> type(connect_matrix[0]) 
> --> out: scipy.sparse.csr.csr_matrix
> 
> 
> obs,clusters,cluster_pv,H=mne.stats.spatio_temporal_cluster_1samp_test( array_of_diffs, connectivity=connect_matrix, n_permuntations=10000)
> --> ValueError: if a connectivity matrix is given, it must be a scipy sparse matrix
> 
> It seems that I am expected to input a different type of scipy sparse matrix for the connectivity argument in the spatio_temporal_cluster_1samp function, but I am unsure which one and how I might do so. 
> 
> Or, if anyone has suggestions for how else I might construct a connectivity matrix to pass into the spatio_temporal_cluster_1samp function, I would greatly appreciate it! 
> 
> Thank you, and best wishes,
> Dillan Cellier 
> 
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