# Missing Data in 3D Connectivity Visualization **URL:** \ **Category:** Support & Discussions\ **Tags:** eeg, visualization\ **Created:** [July 5, 2023, 4:39pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184 "2023-07-05T16:39:09Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![LEPacheco](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/lepacheco/32/2833_2.png) [@LEPacheco](https://mne.discourse.group/u/LEPacheco)\ **Post date:** [July 5, 2023, 4:39pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/1 "2023-07-05T16:39:09Z")
- MNE version: 1.4.2 - MNE - Connectivity version: 0.5.0 - operating system: Windows 10 - Python version: 3.10.9 Hello, I’m using the mne\_connectivity method `plot_sensors_connectivity` and I’m getting the output shown below. However, I’ve noticed that not all the connections are represented and the colorbar has a value range defined. Is there a way to tell the _mne method_ that I would like to visualize all the connections and therefore, change the range of values of the color bar? Second but not least, can I change the colors of the colorbar? My code was based on the example given by MNE itself [https://mne.tools/mne-connectivity/dev/auto\_examples/sensor\_connectivity.html#sphx-glr-auto-examples-sensor-connectivity-py](https://mne.tools/mne-connectivity/dev/auto_examples/sensor_connectivity.html#sphx-glr-auto-examples-sensor-connectivity-py) **My procedure:** - Data acquired with 9 electrodes. - After I calculate the coherence and I got the (81,2) array I’m asigning a variable to the alpha band and another one to the beta band. - The new alpha and beta arrays (9,9) have values ranged from 0.0 to 1.0 ```python epoc_1s = mne.Epochs(canales, event_1s[0], tmin=0, tmax=1, baseline=None) conectividad_1s_coh = spectral_connectivity_epochs(epoc_1s, method='coh', sfreq=Fs, mode='fourier', fmin=f_min, fmax=f_max, faverage=True) matriz_conectividad_coh = conectividad_1s_coh.get_data() mc_alfa_coh = matriz_conectividad_coh[:, 0].reshape(9, 9) ``` - Plotting the connectivity with alpha band information and ONLY values from 0.650 (not the min value) to 0.856 (which is the max value) are shown. ```python easycap_montage = mne.channels.make_standard_montage('easycap-M1') epoc_1s.set_montage(easycap_montage) plot_sensors_connectivity(epoc_1s.info, mc_alfa_coh) ``` ![imagen](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/e/e77ac18f7f8d162f0bce647b52ef5ab9e81d12e3.png) ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [July 11, 2023, 3:04pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/2 "2023-07-11T15:04:38Z")
In version 0.5 the function is hard-coded to only show the 20 strongest connections. The current development version added a new parameter `n_con` to the plotting function so users can control how many connections are shown. Here is the PR that added the new functionality: [[ENH] Added n\_con arg to function call by Avoide · Pull Request #133 · mne-tools/mne-connectivity · GitHub](https://github.com/mne-tools/mne-connectivity/pull/133) You can either upgrade to the current development version (instructions here: [Installation — MNE-Connectivity 0.5.0 documentation](https://mne.tools/mne-connectivity/stable/install.html#installation-via-pip)) or wait for version 0.6 to be released. I don’t know what the release plan is, @adam2392 do you know? ---
**Author:** ![adam2392](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/adam2392/32/35_2.png) [@adam2392](https://mne.discourse.group/u/adam2392)\ **Post date:** [July 11, 2023, 3:28pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/3 "2023-07-11T15:28:52Z")
Hoping to release v0.6 sometime before the end of summer. ---
**Author:** ![LEPacheco](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/lepacheco/32/2833_2.png) [@LEPacheco](https://mne.discourse.group/u/LEPacheco)\ **Post date:** [July 11, 2023, 3:35pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/4 "2023-07-11T15:35:30Z")
Thank you very much! Regarding the question of the colorbar when plotting, can I change the colors? ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [July 11, 2023, 5:03pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/5 "2023-07-11T17:03:41Z")
not easily. If you do: ```python scene = plot_sensors_connectivity(epoc_1s.info, mc_alfa_coh) scene.plotter.scalar_bar.GetLookupTable().apply_cmap("viridis") ``` then you can change the colormap of the bar, but this won’t affect the color of the lines connecting the sensors. I doubt changing both tubes and colorbar _after_ rendering will be easy (or even possible?) so we would need to expose a new option `plot_sensors_connectivity(..., cmap="RdBu")` for it to work. If you want to try to hack it locally, you would need to add the new `cmap` param to the function signature, and then pass it through to `renderer.tube()` here: > cc @larsoner who might know the trick to changing it after rendering. ---
**Author:** ![larsoner](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/larsoner/32/3_2.png) [@larsoner](https://mne.discourse.group/u/larsoner)\ **Post date:** [July 13, 2023, 3:11pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/6 "2023-07-13T15:11:59Z")
It looks like under the hood we use `pyvista.Line` and add a mesh: > So you could look into the relevant PyVista objects and see how they can be modified… ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [July 14, 2023, 9:32pm UTC](https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualization/7184/7 "2023-07-14T21:32:36Z")
feature added in this PR: > > > Addresses https://mne.discourse.group/t/missing-data-in-3d-connectivity-visualiz…ation/7184/4 > > PR Description > \-------------- > > Exposes new \`cmap\` argument in \`plot\_sensors\_connectivity\` > > Merge checklist > \--------------- > > Maintainer, please confirm the following before merging: > > \- \[\] All comments resolved > \- \[\] This is not your own PR > \- \[\] All CIs are happy > \- \[\] PR title starts with \[MRG\] > \- \[\] \[whats\_new.rst\](https://github.com/mne-tools/mne-connectivity/blob/main/doc/whats\_new.rst) is updated > \- \[\] PR description includes phrase "closes \<#issue-number\>"