# Connectivity calculation using PLI **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [March 4, 2020, 10:34am UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101 "2020-03-04T10:34:38Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 4, 2020, 10:34am UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/1 "2020-03-04T10:34:38Z")
External Email - Use Caution Hi, I want to compute connectivity between sources using the PLI metric. As far as I understand it, PLI is computed at the electrode level and not at the source level. Does anyone know how to transform the connectivity matrix between channels into a connectivity matrix between sources? (I've looked at the inverse operator but I have no idea how to apply it to the connectivity matrix). Thanks, Fleur -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20200304/ae6b14dc/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200304/ae6b14dc/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 4, 2020, 8:08pm UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/2 "2020-03-04T20:08:09Z")
External Email - Use Caution hi Fleur, you cannot really transfer PLI from sensor to source. You need to estimate PLI directly in source space eg using parcels. here an example [https://mne.tools/stable/auto\_examples/connectivity/plot\_mne\_inverse\_label\_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py](https://mne.tools/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py) or [https://mne.tools/stable/auto\_examples/connectivity/plot\_mne\_inverse\_psi\_visual.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-psi-visual-py](https://mne.tools/stable/auto_examples/connectivity/plot_mne_inverse_psi_visual.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-psi-visual-py) note that the choice of the parcellation and metric has been the topic of many papers with various recommendations. HTH Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 6, 2020, 10:29am UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/3 "2020-03-06T10:29:28Z")
External Email - Use Caution Hello, Thanks a lot for your help! I actually want to z score connectivities for each subject. Is there a way to compute connectivity for each epoch in the source space? (I mean: a more efficient way than iterating over all epochs) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 6, 2020, 4:09pm UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/4 "2020-03-06T16:09:23Z")
External Email - Use Caution Hi Fleur, our spectral connectivity code does not implement single-trial connectivity, it implements phase statistics across trials. If you want source-level connectivity, you need epochs in source space. To do that in a memory-efficient manner, you can use `return_generator=True` in [https://mne.tools/dev/generated/mne.minimum\_norm.apply\_inverse\_epochs.html](https://mne.tools/dev/generated/mne.minimum_norm.apply_inverse_epochs.html) and then for loop by source localizing one epoch at a time. Best, Denis ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 9, 2020, 11:24am UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/5 "2020-03-09T11:24:27Z")
External Email - Use Caution Hello, I tried source localizing one epoch at a time, and then computing connectivity for each epoch. However, when I average the connectivity matrices over epochs, I do not obtain the same matrix as the one obtained by computing directly connectivity over all epochs in source space. Connectivity matrices for one epoch are made only of 0 and 1. Is there something I'm missing ? ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 10, 2020, 11:29pm UTC](https://mne.discourse.group/t/connectivity-calculation-using-pli/2101/6 "2020-03-10T23:29:09Z")
External Email - Use Caution Hi Fleur, The code in spectral connectivity does not yield any meaningful single-epoch results. At this point, the only valid usage of the function is to compute connectivity across trials. Denis