Deciphering the directionality of information flow in cortical circuits is essential for understanding brain dynamics, learning, and neuroplasticity after injury. However, current noninvasive methods cannot distinguish bottom-up from top-down signals across entire networks, including deep brain regions. Here, we present UltraFast Layer-Resolved Encoding (uFLARE) that combines ultrafast-fMRI with a Layer-based Connective Field (lCF) model to disentangle bottom-up from top-down signaling. Our findings reveal that lCF size, an indicator of information integration, differentiates bottom-up and top-down activity through distinct layer-specific connectivity patterns during spontaneous activity, challenging the previous suggestions that bottom-up signals are solely stimulus-driven. Bottom-up connectivity follows an inverted U-shape, peaking in layer IV, while top-down exhibits a U-shaped pattern, with peaks in layers I and VI. These profiles generalize across sensory pathways (visual, somatosensory, and motor) and reveal injury-induced network reorganization, such as LGN bypassing V1 to provide direct bottom-up input to higher visual areas.

Driven by a period of accelerated progress and recent technical breakthroughs, whole-brain functional neuroimaging in rodents offers exciting new possibilities for addressing basic questions about brain function and its alterations. In response to lessons learned from the human neuroimaging community, leading scientists and researchers in the field convened to address existing barriers and outline ambitious goals for the future. This article captures these discussions, highlighting a shared vision to advance rodent functional neuroimaging into an era of increased impact.

Deciphering the directionality of information flow in cortical circuits is essential for understanding brain dynamics, learning, and neuroplasticity after injury. However, current non-invasive methods cannot distinguish feedforward (FF) from feedback (FB) signals across entire networks, including deep brain regions. Here, we present a novel approach – UltraFast Layer-Resolved Encoding (uFLARE) – that develops ultrahigh spatiotemporal resolution fMRI and a Layer-based Connective Field (lCF) model to disentangle FF from FB signaling. Our findings reveal that lCF size, an indicator of information integration, differentiates FF and FB activity through distinct layer-specific connectivity patterns during spontaneous activity, challenging the notion that FF signals are solely stimulus-driven. FF connectivity follows an inverted U-shape, peaking in layer IV, while FB exhibits a U-shaped pattern, with peaks in layers I and VI. These profiles generalize across sensory pathways (visual, somatosensory, and motor) and reveal injury-induced network reorganization, such as LGN bypassing V1 to provide direct FF input to higher visual areas.

Visual perception can operate in two distinct vision modes-static and dynamic-that have been associated with different neural activity regimes in the superior colliculus (SC). However, the associated pathway-wide mechanisms remain poorly understood, especially in terms of corticotectal and tectotectal feedback upon encoding the continuity illusion during the dynamic vision mode. Here, we harness functional MRI combined with rat brain lesions to investigate whole-pathway neural interactions in the dynamic vision mode. We find a push-pull mechanism embodying contralateral suppression of SC activity opposing positive ipsilateral neural activation upon monocular visual stimulation. Cortical amplification is confirmed through cortical lesions, while further lesioning the ipsilateral SC leads to a boost in the contralateral SC negative signals, suggesting a tectal origin for the push-pull interaction. These results highlight hitherto unreported frequency-dependent modulations in the tectotectal pathway and further challenge the notion that intertectal connections solely serve as reciprocal inhibitory mechanisms for avoiding visual blur during saccades.

The role of subcortical structures in binaural integration is of great interest for auditory processing. The inferior colliculus (IC) is the main auditory midbrain center where ascending and descending auditory projections converge, which was suggested to encode auditory information via a push-pull mechanism (a coordinated antagonistic neural mechanism for adaptive response control) between the two ICs. However, the origin of this push-pull mechanism in the brain and how it interacts with other upstream/downstream subcortical areas are still a matter of great debate. Here, we harness functional MRI (fMRI) in combination with IC lesions in the rat to dissect the push-pull interaction from a pathway-wide perspective. We find evidence for the push-pull mechanism in IC through opposing negative/positive fMRI signals in the ipsilateral/contralateral ICs upon monaural stimulation. By unilaterally lesioning the corresponding contralateral IC, we demonstrate the necessity of collicular integrity and intercollicular interactions for the push-pull interaction. Using binaural stimulation and IC lesions, we show that the push-pull interaction is exerted also in binaural processing. Finally, we demonstrate that, at least at the population level revealed by fMRI, the main push-pull interactions occur first at the IC level, and not earlier, and that the outcome of the push-pull "calculation" is relayed downstream to the medial geniculate body (MGB). This dissection of the push-pull interaction sheds light into subcortical auditory function.

The visual continuity illusion involves a shift in visual perception from static to dynamic vision modes when the stimuli arrive at high temporal frequency, and is critical for recognizing objects moving in the environment. However, how this illusion is encoded across the visual pathway remains poorly understood, with disparate frequency thresholds at retinal, cortical, and behavioural levels suggesting the involvement of other brain areas. Here, we employ a multimodal approach encompassing behaviour, whole-brain functional MRI, and electrophysiological measurements, for investigating the encoding of the continuity illusion in rats. Behavioural experiments report a frequency threshold of 18±2 Hz. Functional MRI reveal that superior colliculus signals transition from positive to negative at the behaviourally-driven threshold, unlike thalamic and cortical areas. Electrophysiological recordings indicate that these transitions are underpinned by neural activation/suppression. Lesions in the primary visual cortex reveal this effect to be intrinsic to the superior colliculus (under a cortical gain effect). Our findings highlight the superior colliculus’ crucial involvement in encoding temporal frequency shifts, especially the change from static to dynamic vision modes.

AbstractThe role of subcortical structures in binaural integration is of great interest for auditory processing. The inferior colliculus (IC) is the main auditory midbrain center where ascending and descending auditory projections converge, which was suggested to encode auditory information via a push-pull mechanism between the two ICs. However, the origin of this push-pull mechanism in the brain and how it interacts with other upstream/downstream subcortical areas is still a matter of great debate. Here, we harness functional MRI (fMRI) in combination with IC lesions in the rat to dissect the push-pull interaction from a pathway-wide perspective. We find evidence for the push-pull mechanism in IC through negative/positive fMRI signals in the ipsilateral/contralateral ICs upon monaural stimulation. By unilaterally lesioning the corresponding contralateral IC, we demonstrate the necessity of collicular integrity and intercollicular interactions for the push-pull interaction. Using binaural stimulation and IC lesions, we show that the push-pull interaction is exerted also in binaural processing. Finally, we demonstrate that, at least at the population level revealed by fMRI, the main push-pull interactions occur first at the IC level, and not earlier, and that the outcome of the push-pull “calculation” is relayed downstream to MGB. This dissection of the push-pull interaction sheds light into subcortical auditory function.

When visual stimuli are presented at a sufficiently high temporal frequency, visual perception shifts from the static to dynamic vision mode, thereby facilitating a continuity illusion which is key for correctly identifying continuous and moving objects and placing them in the context of the surrounding environment. However, how this continuity illusion is encoded along the entire visual pathway remains poorly understood, with disparate Flicker Fusion Frequency (FFF) thresholds measured at retinal, cortical, and behavioural levels. Here, we hypothesized that these disparities may suggest that other brain areas may be involved in encoding the shift from static to dynamic vision modes. We employ a comprehensive approach encompassing behavioural measurements, whole brain activation mapping with high fidelity functional MRI (fMRI), and local electrophysiological validation for studying the mechanisms underlying the shift from static to dynamic vision modes in the rat. Our behavioural measurements reported an FFF threshold proxy of 18±2 Hz. At the network level, functional MRI revealed that the superior colliculus (SC) exhibits marked signal transitions from positive to negative fMRI signal regimes at the behaviourally measured FFF threshold surrogates, with a strong linear correlation between fMRI signal and behaviour, while thalamic and cortical visual areas displayed a significantly poorer correlation with the behaviour. fMRI-driven neurometric curves approximated the behavioural psychometric curve in SC but not in the other visual areas. Electrophysiological recordings in SC suggested that these fMRI signals transitions arise from strong neural activation/suppression at low/high frequency regimes, respectively, and that a transition between these regimes occurs around the measured FFF threshold proxies. Lesions in V1 further reinforced that these transitions originate in SC. Combined, our data suggests a critical role for SC in encoding temporal frequency discriminations, in particular the shifts from the static to the dynamic vision modes.

Encoding and processing sensory information is key to understanding the environment and to guiding behavior accordingly. Characterizing the behavioral and neural correlates of these processes requires the experimenter to have a high degree of control over stimuli presentation. For auditory stimulation in animals with relatively large heads, this can be accomplished by using headphones. However, it has proven more challenging in smaller species, such as rats and mice, and has been only partially solved using closed-field speakers in anesthetized or head-restrained preparations. To overcome the limitations of such preparations and to deliver sound with high precision to freely moving animals, we have developed a set of miniature headphones for rats. The headphones consist of a small, skull-implantable base attached with magnets to a fully adjustable structure that holds the speakers and keeps them in the same position with respect to the ears.

Monocular visual stimulation with short inter-stimulus intervals (ISIs) evokes (i) negative BOLD responses (NBRs) in the contralateral superior colliculus (cSC), and (ii) positive BOLD responses (PBRs) in the ipsilateral superior colliculus (iSC). This pattern suggests a potential "push-pull" mechanism between SCs possibly evoked by (mostly inhibitory) tectotectal projections. Here, we mapped activity in the entire visual pathway using fMRI, and modulated cSC inputs through lesions in visual cortex and SC to dissect collicular communication mechanisms. While, cortical context potentiated a putative “push-pull” mechanism, further silencing of iSC resulted in PBRs in cSC, suggesting that iSC exerts suppression on cSC.

Although Weber's law is the most firmly established regularity in sensation, no principled way has been identified to choose between its many proposed explanations. We investigated Weber's law by training rats to discriminate the relative intensity of sounds at the two ears at various absolute levels. These experiments revealed the existence of a psychophysical regularity, which we term time-intensity equivalence in discrimination (TIED), describing how reaction times change as a function of absolute level. The TIED enables the mathematical specification of the computational basis of Weber's law, placing strict requirements on how stimulus intensity is encoded in the stochastic activity of sensory neurons and revealing that discriminative choices must be based on bounded exact accumulation of evidence. We further demonstrate that this mechanism is not only necessary for the TIED to hold but is also sufficient to provide a virtually complete quantitative description of the behavior of the rats.

The accuracy of the neural code depends on the relative embedding of signal and noise in the activity of neural populations. Despite a wealth of theoretical work on population codes, there are few empirical characterizations of the high-dimensional signal and noise subspaces. We studied the geometry of population codes in the rat auditory cortex across brain states along the activation-inactivation continuum, using sounds varying in difference and mean level across the ears. As the cortex becomes more activated, single-hemisphere populations go from preferring contralateral loud sounds to a symmetric preference across lateralizations and intensities, gain-modulation effectively disappears, and the signal and noise subspaces become approximately orthogonal to each other and to the direction corresponding to global activity modulations. Level-invariant decoding of sound lateralization also becomes possible in the active state. Our results provide an empirical foundation for the geometry and state-dependence of cortical population codes.

Weber’s law states that the discriminability between two stimulus intensities depends only on their ratio. Despite its status as the cornerstone of psychophysics, the mecha-nisms underlying Weber’s law are still debated, as no principled way exists to choose between its many proposed alternative explanations. We studied this problem training rats to discriminate the lateralization of sounds of different overall level. We found that the rats’ discrimination accuracy in this task is level-invariant, consistent with Weber’s law. Surprisingly, the shape of the reaction time distributions is also level-invariant, implying that the only behavioral effect of changes in the overall level of the sounds is a uniform scaling of time. Furthermore, we demonstrate that Weber’s law breaks down if the stimulus duration is capped at values shorter than the typical reaction time. Together, these facts suggest that Weber’s law is associated to a process of bounded evidence accumulation. Consistent with this hypothesis, we show that, among a broad class of sequential sampling models, the only robust mechanism consistent with reaction time scale-invariance is based on perfect accumulation of evidence up to a constant bound, Poisson-like statistics, and a power-law encoding of stimulus intensity. Fits of a minimal diffusion model with these characteristics describe the rats performance and reaction time distributions with virtually no error. Various manipulations of motivation were unable to alter the rats’ psychometric function, demonstrating the stability of the just-noticeable-difference and suggesting that, at least under some conditions, the bound for evidence accumulation can set a hard limit on discrimination accuracy. Our results establish the mechanistic foundation of the process of intensity discrimination and clarify the factors that limit the precision of sensory systems.

Negative BOLD responses (NBRs) in rat Inferior Colliculus (IC) were recently observed upon monaural auditory stimulation, but their origins and importance remain poorly understood. Intercollicular communication is proposed as a prominent mechanism for auditory processing, including sound localization/lateralization & in gain control regulation. Here, we investigated intercollicular interaction via monoaural stimulation at 9.4T. Rats exhibited NBRs in the ipsilateral IC and positive BOLD responses (PBRs) in the contralteral IC. When the contralateral hemisphere was lesioned, the NBRs vanished in the ipsilateral IC. Our findings suggest that intercollicular interaction is essential for ipsilateral negative BOLD responses and for auditory processing.

The role of the rodent inferior colliculus (IC) in binaural integration is of great interest especially for sound localization and processing of interaural level difference (ILD). Yet, many IC underlying mechanisms remain unclear. Here, we find evidence for a push/pull mechanism in IC, with contralateral (positive BOLD) activity exerting dominance over ipsilateral (negative BOLD) activity, possibly as means of a sound localization/lateralization.

The underlying sources of negative BOLD responses (NBRs) are still debated. Here, we show rat superior colliculus (SC) NBRs associated with visual stimulation at short inter-stimulus intervals (ISIs) along with decreases in power of local field potentials and multi-unit activity signals measured in this region. This hints to neuronal suppression, possibly due to impossibility of complete excitability recovery upon short ISIs, associated with NBRs. Moreover, both NBRs and electrophysiological power time profiles reveal one peak after stimulus started and another when it ceased, highlighting the SC nature of detecting "brightness changes" when individual flashes are no longer perceivable.