[Mne_analysis] using find_ch_connectivity for spatio-temporal clustering

[Dillan Cellier]

        External Email - Use Caution        

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:

>         External Email - Use Caution
>
> 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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