Ongoing thoughts at rest reflect functional brain organization and behaviour.

Resting-state functional connectivity (rsFC)-brain connectivity observed when people rest with no external tasks-predicts individual differences in behaviour. Yet, rest is not idle; it involves streams of thoughts. Are these ongoing thoughts reflected in FC and do they contribute to the relationship between rsFC and behaviour? Here, to test this question, we used an annotated rest paradigm where participants rated and verbally described their thoughts after each rest period during functional MRI (N = 60). Our findings revealed rich and idiosyncratic thoughts across individuals. Similarity in thoughts was associated with more similar FC patterns within and across individuals. In addition, both thought ratings and topics could be decoded from FC. Furthermore, neuromarkers of these thoughts generalized to unseen individuals in the Human Connectome Project dataset (N = 908), where decoded thought patterns during rest predicted positive vs negative trait-level individual differences. Together, our findings reveal that ongoing thoughts at rest are reflected in brain dynamics and these network patterns predict everyday cognition and experiences. Understanding subjective in-scanner experiences is thus crucial in characterizing the relationship between individual differences in functional brain organization and behaviour.