[Mne_analysis] using find_ch_connectivity for spatio-temporal clustering

Denis A. Engemann denis-alexander.engemann at inria.fr
Wed Jul 31 17:27:04 EDT 2019
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No problem. 
You were close to finding it with your type check.

Best,
Denis

> On Jul 31, 2019, at 11:21 PM, Dillan Cellier <cellierdillan at gmail.com> wrote:
> 
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> 
> 
> Oh! What a silly oversight. Thank you much for catching that, Denis!
> 
> On Wed, Jul 31, 2019 at 4:20 PM Denis A. Engemann <denis-alexander.engemann at inria.fr> wrote:
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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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