[Mne_analysis] cluster permutation connectivity matrix

[Yvonne Fonken]

Hi Alex,

Thank you for your reply.

This is my code, with two versions of a diagonal connectivity matrix (using
version 14.1 of MNE):
# Implement cluster permutation
numChan = Data.shape[1] # Data is shaped: Trials (115) x channels (217) x
timepoints (30) numpy array
#connectivity =  np.diagflat( range(0,numChan), k = 0)
connectivity =  np.diagflat( np.ones((1,numChan)), k = 0) # N x N diagonal
matrix with N being # of electrodes
TestData = np.swapaxes(Data, 1,2) # trials x time x space (electrodes)
T_obs, clusters, p_values, H0 =
mne.stats.permutation_cluster_1samp_test(TestData, n_permutations = 500,
tail = 0, connectivity = connectivity)

Both versions of the connectivity matrix now give me the following error:
'numpy.ndarray' object has no attribute 'tocsr'

Thanks,
Yvonne

On Tue, Sep 19, 2017 at 1:02 AM, Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

> Hi Yvonne
>
> I would have said that a sparse diagonal matrix should work.
>
> can you share the code snippet you used?
>
> Alex
>
>
> On Tue, Sep 19, 2017 at 3:17 AM, Yvonne Fonken <yfonken at berkeley.edu>
> wrote:
> > Hi all,
> >
> > I am trying to apply the cluster permutation function in MNE on
> intracranial
> > data (electrodes by time points), either by using
> > mne.stats.permutation_cluster_test, or
> > mne.stats.permutation_cluster_1samp_test. In this case, I do not want to
> > cluster across electrodes, but I want to include this dimension in order
> to
> > correct for multiple comparisons.
> >
> > My question is: how do I specify to only cluster over time, and not
> > electrodes? Can I do this using the connectivity matrix, and if yes, what
> > would a connectivity matrix look like when all electrodes do not have
> > neighbors? I've tried using diagonal matrices already, but I still get
> > clusters spanning multiple electrodes.
> >
> > Thanks,
> > Yvonne
> >
> > --
> > Yvonne Fonken
> > PhD Candidate
> > Helen Wills Neuroscience Institute
> > University of California, Berkeley
> >
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-- 
Yvonne Fonken
Graduate student
Helen Wills Neuroscience Institute
University of California, Berkeley
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