Questions about the usage of stats.statscluster

[parkinsonlyn]

Hi HyPyP team, thank you for your great efforts. Having read the introductory paper and the tutorial, I still have some questions regarding the usage of stats.statscluster to achieve cluster-level permutation and hoping to receive some advice.

As I have already calculated the inter-brain connectivity between all dyads using Ccorr, and have sliced and stored the inter-brain part of the matrix. Now I would like to see whether there are differences between two groups in inter-brain connectivity. The other arguments seem no problem except for ch_con_freq, which needs to be calculated for the metaconnectivity (as I did not calculate PSD or CSD prior). Thus according to the tutorial, the calculation is as follow:

# targeted frequency as Theta
freqs_mean = np.arange(4, 8)

# merge two example data to cal. indicies
subjall = utils.merge(subj0, subj1)

# cal. indicies of inter-brain connectivity
ind = analyses.indices_connectivity_interbrain(subjall)

# cal. the connectivity matrix from the single participant
con = stats.con_matrix(subj0, freqs_mean)

# cal. the inter-brian metaconnectivity
meta = stats.metaconn_matrix_2brains(ind, con.ch_con, freqs_mean)

# permutation
dyad_all = [group1, group2]
sig = stats.statscluster(data = dyad_all, 
                   test = 'ind ttest', 
                   factor_level = None,
                   ch_con_freq = scipy.sparse.bsr_matrix(meta[0]),
                   tail = 0, 
                   n_permutations = 5000,
                   alpha = 0.05)

Although the above code is working, is it the right way to conduct the statistical analysis? It seems the connectivity matrix was not influenced by the frequencies (α/θ/β...) but only the numbers of bins in the frequency ROI.

Also, in the section of "Comparing Inter-brain connectivity values to random signal" of the getting_started, the argument was set ch_con_freq=None, what's the difference between ch_con_freq being set and remitted?

Thanks a lot. Richard

[etherealsunshine]

Hi! I'll try my best to get back to you with the rest of your questions, but Setting ch_con_freq to None, as seen in the tutorial section, means that the function is not using a specific connectivity matrix for the permutation test. Instead, it compares the observed inter-brain connectivity values to a random signal.

[parkinsonlyn]

Hi! I'll try my best to get back to you with the rest of your questions, but Setting ch_con_freq to None, as seen in the tutorial section, means that the function is not using a specific connectivity matrix for the permutation test. Instead, it compares the observed inter-brain connectivity values to a random signal.

Thanks! Looking forward to your reply for the rest of the questions.