Hi! I would like to plot a topomap from obtained psd_welch() values. However I don’t know how to find the channel and position information, so I tried to do the following using a Layout: [Captura de pantalla 2021-10-05 a las 14.33.32] But I couldn’t manage to fit the sensors into the blue circl…

Hi @guiomar , I’m not an MEG guy, so I never used layouts, but here are my thoughts: The layout you read has center away from (0, 0, 0): laypos.mean(axis=0) # array([0.47688583, 0.46079796, 0.03376805, 0.02814004]) so the position of the sensors that you see in the topomap is correct. The layout…

you have an issue with the head coordinate system (defined with 3 fiducials) and your channel locations. did you hack the measure info? was there an issue during acquisition? Alex

Thnaks! It’s one subject of the camcan, so I’ll have a closer look at these details

Hi @agramfort ! I’ve been reviewing it but in the code I’m only using the channels positions used in ‘Vectorview-all.lout’ layout included in MNE: layout='Vectorview-all.lout' laypos = mne.channels.read_layout(layout).pos So I’m only passing this to the plot_topomat function. If a simplified versi…

Thank you @mmagnuski !! That’s super useful. I dind’t know how to get the channel positions info from the raw meg data after applying the psd_welch(), so that’s way I tried to go with the layout. How do people usually do this? Sorry I didn’t want you to change the things, I think with this trick I…

[image] mmagnuski: If layouts are supposed to work out of the box when their .pos is passed to mne.viz.plot_topomap then I’d consider the behavior reported by @guiomar to be a bug. WDYT? I think we had a related discussion at [image] mne.viz.plot_topomap - align data to head…

[image] guiomar: Or if you show me a more efficient way to do it, I’d be happy to learn! I always pass the info to mne.viz.plot_topomap. So if I have epochs object I then do mne.viz.plot_topomap(some_data, epochs.info). I only used this for EEG, but I think it should work for MEG as well. Let…

Thanks @richard for the related discussion! @mmagnuski I’m working with resting data which have not been epoched. And the psd_welch() function just returns an array of values, so no more info about the channels. How should I epoch rest data, with maybe a fixed window length? do you have any exampl…

[image] guiomar: How should I epoch rest data, with maybe a fixed window length? do you have any example I could look at? Thanks a lot! If you have raw object pass raw.info as channel positions.

Thanks @mmagnuski With the tip you gave me about centering the layout, the issue is solved, So I’ll close the thread :slight_smile: Thanks once more for your super fast responses!

Hello @guiomar , I’ve answered to a related question you posted a while back, but I believe this could resolve your issue without having to deal with a layout manually: [image] extract values from figures 💬 Support & Discussions Hello @guiomar , to plot topographies of PSD…

topomap with layout

Support & Discussions

richard (Richard Höchenberger) October 6, 2021, 9:17am 7

I think we had a related discussion at

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Plotting topomap using a custom magnetometer layout Support & Discussions	2	317	November 18, 2022
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topomap with layout

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