MNE version: 1.11.0 operating system: WSL: Ubuntu-22.04 Hi everyone! I’m a young researcher very new to MEG analysis and MNE… looking for some help :blush: I’m currently adapting an MEG pre-processing pipeline written in Neuropycon to MNE-BIDS-Pipeline. I’m working with already BIDSified CTF re…

[image] LeonardoMelloni: why EEG channels were initially taken into account even if I set ch_types = [‘meg’]? They shouldn’t have been, this seems like a bug. I have a vague recollection of hitting something similar in the past months and fixing it, are you on latest mne-bids-pipeline main? …

Hi @LeonardoMelloni and welcome to the forum! [image] LeonardoMelloni: As far as I understood, during ICA the experimental data is compared to emptyroom and given that they have different compensation grades the error occurs. @larsoner , should we call Raw.apply_gradient_compensation() somewh…

I don’t think we (as in MNE-Python) should… I think the user probably should before trying to apply ICA. Maybe we need to improve the error message here

@larsoner But this is in MNE-BIDS-Pipeline. So either we should handle this automatically, or it’s something that should be taken care of when converting the data to BIDS, don’t you think?

Thanks for your replies guys, they allowed me to better understand the issue. Now I’ll try to use mne.io.Raw.apply_gradient_compensation() during BIDSification and see how it goes. Anyway, are you considering to implement it in the pipeline?

Hi! I’m still not sure what the right approach is here, honestly. It appears the BIDS specification currently doesn’t cover this. Hence, I would assume it’d be better to apply the compensation before converting to BIDS. @sappelhoff , perhaps this should even live in MNE-BIDS?

[image] richard: Hence, I would assume it’d be better to apply the compensation before converting to BIDS. Yeah it’s weird to me that they don’t all have the same compensation grade. But probably something that MNE-BIDS-Pipeline could easily handle with a new gradient_compensation: int | None…

[image] larsoner: @LeonardoMelloni want to try adding it to MNE-BIDS-Pipeline and opening a PR? Or if you want, I could try opening a PR and you could test it on your data. [image] richard: I would assume it’d be better to apply the compensation before converting to BIDS. I don’t th…

[image] LeonardoMelloni: I’m considering to first correct for it in the BIDSification I’m working on making a script for “re-BIDSifying” the data imposing the compensation grade to 0 for experimental data. Now I’m running into a strange behavior that I think can be summed up with the followin…

Hmm I’m not sure about how it writes data… I doubt MNE-BIDS is smart enough to be able to write a different compensation grade :frowning: I don’t think the modifications for MNE-BIDS-Pipeline will be too bad actually. Can you open a quick issue on GitHub · Where software is built so I don’t forget …

Done. Thank you. I went over the problem by changing the compensation grade of emptyroom from 0 to 3 during BIDSification and writing it back imposing format=’FIF’ to make everything work fine. Anyway I got an other error during ICA on emptyroom because it had a different number of EEG channels wi…

Error: Compensation grade of ICA (3) and Raw (0) do not match

Support & Discussions

LeonardoMelloni (Leonardo Melloni) March 16, 2026, 2:17pm 13

This seems to be working. But with the new version I’m running into new problems. I thought could be worth to open a new topic

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Error: Compensation grade of ICA (3) and Raw (0) do not match

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