How Are Raw Annotations Handled During Source Reconstruction?

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Hello MNE team,

I hope this question isn’t already covered in the documentation – I’ve been searching through it but couldn’t find a clear answer. As part of my resting-state pipeline, I perform a final visual quality-control step where I manually annotate segments of continuous data for rejection. My question is: how are these annotations handled during source reconstruction?

I know that several preprocessing functions respect annotations when reject_by_annotation=True. However, during source estimation, I don’t see any parameter that explicitly enables, disables, or otherwise controls the inclusion/exclusion of these annotated time segments.

Could you clarify whether source reconstruction routines implicitly ignore annotated segments, or whether additional steps are required to ensure that noisy segments are excluded from the inverse solution?

Thank you very much for your guidance.

Best regards,

Santiago

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any segments with a label starting with BAD are excluded by default. Others are included by default.

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Awesome! Thank you very much!! =)

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