About the transformation of matrix connections and non-parametric permutation test

[Hanxiaoke]

Dear Brainstorm Team,

I want to conduct a non-parametric permutation test to assess the differences in connectivity values of theta band PTE brain networks between two groups of participants. However, after transforming the PTE connectivity matrix into a 68×68 matrix, I carried out some processing. How should I revert this matrix back to a 4624×1 vector format to enable the use of the following code for statistical analysis? Additionally, if I use the matrix processed by myself, can I change "'freqrange', [1, 80]" to "'freqrange', [4, 8]"?

Looking forward to your reply. I would be immensely grateful for any assistance you can provide.

sFiles = {...
    'timefreq_connectn_average_230902_1836.mat', ...
    'timefreq_connectn_average_230902_1836.mat',...
};

sFiles2 = {...
    'timefreq_connectn_average_230902_1836.mat', ...
    'timefreq_connectn_average_230902_1836.mat',...
};

% Process: Perm t-test equal [-2000ms,2000ms 1-80Hz] H0:(A=B), H1:(A<>B)
sFiles = bst_process('CallProcess', 'process_test_permutation2', sFiles, sFiles2, ...
                                  'timewindow', [-2, 2], ...
                                  'freqrange', [1, 80], ...
                                  'rows', '', ...
                                  'isabs', 0, ...
                                  'avgtime', 1, ...
                                  'avgrow', 0, ...
                                  'avgfreq', 0, ...
                                  'matchrows', 0, ...
                                  'iszerobad', 1, ...
                                  'test_type', 'ttest_equal', ...
                                  'randomizations', 1000, ...
                                  'tail', 'two');

ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);

Yours,
Xiaoke

[Raymundo.Cassani]

Connectivity matrices are reshaped before saved in the TF field of the their .mat.

As such, if you want to carry out further processing outside of Brainstorm it is necessary to reshape them (connectivity matrix > TF field) and get them (TF > connectivity matrix). Check these posts about these links towards the documentation and related forum topics:

Documentation:
https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity#On_the_hard_drive

Related forum topics:

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@Hanxiaoke

Additionally, if I use the matrix processed by myself, can I change "'freqrange', [1, 80]" to "'freqrange', [4, 8]"?

You need to use values make sense for the field Freqs in the custom connectivity file