@Sylvain
I'm not sure I understand the pipeline you describe here.
The connectivity functions (e.g. correlation) are not equipped to handle time-frequency files (e.g. Hilbert process results) in input. This is not a easy feature to add.
All the connectivity measures that use the Hilbert transform do it internally, see examples below:
- Amplitude Envelope Correlation: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/connectivity/bst_connectivity.m#L437
- Phase Locking Value: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/connectivity/bst_connectivity.m#L497
- PLV (time): https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/connectivity/bst_connectivity.m#L539
- Phase Transfer Entropy: https://github.com/brainstorm-tools/brainstorm3/blob/master/external/fraschini/PhaseTE_MF.m#L67
- tPAC:
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_pac_ir_dynamic.m#L804
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_pac_dynamic.m#L675