Biology subjects

Stirnberg, R.

Publications and source records attributed to Stirnberg, R..

11 recordsLinked to original sources

bioRxiv2026

Peripheral Nerve Stimulation Optimized Pulses for EPI (POPE) allows high-resolution fMRI

PurposeRecent improvements in MRI gradient design and amplifiers, advanced MRI scanners are now routinely utilizing slew rates of several hundred T/m/s. However, full gradient performance cannot be exploited in high-resolution EPI due to peripheral nerve stimulation (PNS) limits. We aim to characterize and mitigate these PNS constraints using a simple sequence modification: PNS-optimized EPI gradient pulse shapes. MethodsPNS-Optimized Pulses for EPI (POPE): we selectively reduce the slew rate of gradient pulses at periods of high predicted PNS spikes, while leaving the rest of the waveform unchanged. PNS sensation was evaluated. ResultsPOPE allows 7%-35% faster imaging of EPI protocols resolutions of 1mm-0.3mm resolutions without exceeding predicted PNS. With such improvements, POPE allows robust 0.3 mm isotropic fMRI protocols that would have exceeded safety limits without it. ConclusionPOPE facilitates locally precise fMRI activation mapping on clinical 7T scanners at spatial resolution that were previously unattainable due to PNS limitations.

neuroscience↗

bioRxiv2025

Seeing more than schemas: the vmPFC represents imagery- rich mental scenarios

Mental imagery varies dramatically across individuals, from vivid scene construction to the complete absence of visual experience, as seen in aphantasia. While the ventromedial prefrontal cortex (vmPFC) is traditionally associated with abstract, schematic representations, emerging theories suggest it may also contribute to constructing vivid, visual mental content. To test this, we developed a novel 7T fMRI experiment varying imagery demands across conditions: Prior to scanning, participants memorized richly detailed scenarios, more constrained, stationary objects, and finally semantic definitions for each of three abstract German words (e.g., hope). During fMRI and eye-tracking, the same word was presented across trials, but participants vividly re-engaged with one of three distinct representations (i.e., scenarios, objects, and definitions), allowing for comparison across richly different cognitive modes triggered by identical visual input. Univariate analyses confirmed previous findings; highlighting the roles of the vmPFC, hippocampus, parahippocampal cortex, and visual-perceptual cortex in imagery-rich scenario construction. We further performed multivoxel pattern analysis (MVPA) to examine distributed neural representations, which can reveal the informational content of mental imagery beyond activation magnitude. Critically, the vmPFC was the only brain region where MVPA classifier accuracy was higher for scenario construction than for object and abstract conditions, directly supporting our hypothesis that the vmPFC encodes imagery-rich details rather than solely abstract, schematic information. Eye movement variability also distinguished between conditions. These findings advance our understanding of vmPFC function, emphasising its role in representing vivid mental content. HighlightsO_LI{middle dot} vmPFC distinctly represents imagery-rich scenarios in MVPA analysis C_LIO_LIUnivariate fMRI reveals increased HC and PHC activity during scenario construction C_LIO_LIEye movements vary by imagery type, distinguishing scenarios from objects and definitions C_LI

neuroscience↗

bioRxiv2025

Elucidating directed neural dynamics of scene construction across memory and imagination

Autobiographical memory (AM) and imagination both rely on the brains ability to construct vivid, coherent mental representations of past or imagined experiences. A central cognitive process underlying these functions is scene construction--the mental generation of spatially organized, imagery-rich representations of environments. Using ultra-high field 7T fMRI combined with Dynamic Causal Modeling (DCM), we examined directed effective connectivity among key nodes of the default mode network: the ventromedial prefrontal cortex (vmPFC), hippocampus, and precuneus during object imagery, single-scene construction, and AM retrieval. Our results revealed distinct patterns of network dynamics depending on task demands. During AM retrieval, effective connectivity was characterized by vmPFC-driven top-down modulation primarily targeting the precuneus, supporting the temporal and self-relevant structuring of episodic memory. In contrast, extended scenario imagination engaged hippocampal bidirectional influences with both vmPFC and precuneus, reflecting the dynamic simulation and integration of unfolding events. Single Scene construction shifted network leadership to the precuneus, which exerted modulatory effects on both vmPFC and hippocampus, consistent with its pivotal role in spatial integration and the generation of coherent mental scenes. Object imagery showed minimal stable connectivity within this network, suggesting limited engagement of the hippocampal-default mode circuit during simpler visual representations. Together, our findings highlight a flexible, task-dependent reorganization of effective connectivity within the vmPFC- hippocampus-precuneus network during the construction of rich mental experiences. Scene construction emerges as a unifying mechanism linking memory and imagination, with the direction and strength of neural interactions adapting according to whether temporal or spatial demands predominate. HighlightsO_LIAutobiographical memory is reflected by vmPFC-driven effective connectivity C_LIO_LIEffective connectivity varies flexibly amongst vmPFC, hippocampus and precuneus C_LIO_LIScene construction emerges as a core process across memory and imagination C_LI

neuroscience↗

bioRxiv2025

From single scenes to extended scenarios: the role of the ventromedial prefrontal cortex in the construction of imagery-rich events

Mental events are fundamental to daily cognition, including the recollection of past experiences, the anticipation of future scenarios, and engagement in imaginative, fictitious thought. Typically, these temporally extended mental events unfold within coherent spatial contexts, rich in naturalistic scenes and objects. However, there remains a significant gap in understanding how these events are represented in the brain. This study aimed to investigate the neural patterns involved in the construction of temporally extended mental events. Using ultra-high field functional magnetic resonance imaging, we examined brain regions previously implicated in this cognitive process, including the ventromedial prefrontal cortex (vmPFC), hippocampus, and posterior neocortex. We employed a novel experimental paradigm in which participants engaged in three forms of mental imagery: single objects (e.g., "a black espresso"), single scenes (e.g., "a busy cafe"), and extended scenarios (e.g., "meeting a friend for coffee"). We identified a shared neural network - comprising the vmPFC, hippocampus, and posterior neocortex - engaged across all forms of mental imagery. However, we observed a hierarchical organization in their contributions: the posterior neocortex supported the construction of objects, scenes, and scenarios, while the hippocampus primarily contributed to scenes and scenarios. The vmPFC exhibited a stepwise increase in activation, peaking during scenario construction. These findings suggest that the construction of mental events emerges from the close interaction of perceptual details provided by the posterior neocortex, spatial coherence from the hippocampus, and the integration of those elements into a coherent, temporally extended mental event by the vmPFC - the "movies" of the mind.

neuroscience↗

bioRxiv2024

T1234: A distortion-matched structural scan solution to misregistration of high resolution fMRI data

PurposeHigh-resolution fMRI at 7T is challenged by suboptimal alignment quality between functional data and structural scans. This study aims to develop a rapid acquisition method that provides distortion-matched, artifact-mitigated structural reference data. MethodsWe introduce an efficient sequence protocol termed T1234, which offers adjustable distortions. This approach involves a T1-weighted 2-inversion 3D-EPI sequence with four spatial encoding directions optimized for high-resolution fMRI. A forward Bloch model was used for T1 quantification and protocol optimization. Twenty participants were scanned at 7T using both structural and functional protocols to evaluate the utility of T1234. ResultsResults from two protocols are presented. A fast distortion-free protocol reliably produced whole-brain segmentations at 0.8mm isotropic resolution within 3:00-3:40 minutes. It demonstrates robustness across sessions, participants, and three different 7T SIEMENS scanners. For a protocol with geometric distortions that matched functional data, T1234 facilitates layer-specific fMRI signal analysis with enhanced laminar precision. ConclusionThis structural mapping approach enables precise registration with fMRI data. T1234 has been successfully implemented, validated, and tested, and is now available to users at our center and at over 50 centers worldwide.

neuroscience↗

bioRxiv2024

Fuzzy ripple artifact in high resolution fMRI: identification, cause, and mitigation

PurposeHigh resolution fMRI is a rapidly growing research field focused on capturing functional signal changes across cortical layers. However, the data acquisition is limited by low spatial frequency EPI artifacts; termed here as Fuzzy Ripples. These artifacts limit the practical applicability of acquisition protocols with higher spatial resolution, faster acquisition speed, and they challenge imaging in lower brain areas. MethodsWe characterize Fuzzy Ripple artifacts across commonly used sequences and distinguish them from conventional EPI Nyquist ghosts, off-resonance effects, and GRAPPA artifacts. To investigate their origin, we employ dual polarity readouts. ResultsOur findings indicate that Fuzzy Ripples are primarily caused by readout-specific imperfections in k-space trajectories, which can be exacerbated by inductive coupling between third-order shims and readout gradients. We also find that these artifacts can be mitigated through complex-valued averaging of dual polarity EPI or by disconnecting the third-order shim coils. ConclusionThe proposed mitigation strategies allow overcoming current limitations in layer-fMRI protocols: O_LIAchieving resolutions beyond 0.8mm is feasible, and even at 3T, we achieved 0.53mm voxel functional connectivity mapping. C_LIO_LISub-millimeter sampling acceleration can be increased to allow sub-second TRs and laminar whole brain protocols with up to GRAPPA 8. C_LIO_LISub-millimeter fMRI is achievable in lower brain areas, including the cerebellum. C_LI

neuroscience↗

bioRxiv2024

Neural representation of direct-to-reverberant energy ratio in recorded and simulated binaural room auralizations

In complex acoustic environments, sound localization involves the integration of numerous interrelated auditory and cognitive cues, making it challenging to understand their relationship to brain activity. Here, we use virtual acoustics to probe the brains response to auditory distance cues in a realistic environment. We developed a system to record the actual MRI environment, simulated the same room with different degrees of accuracy, then presented sounds at one of two locations in the room. We implemented a novel auditory fMRI sequence to record brain activity. Despite only minor differences in acoustics between the auralizations, it was possible to decode all three rooms from brain activity. A systematic analysis revealed that the direct-to-reverberant energy ratio (DRR) drove brain activity differences between auralizations, centered on the posterior auditory cortex (AC). The results provide strong evidence that the posterior AC processes DRR for spatial auditory perception. Impact statementA novel fMRI sequence and recording technique are combined with virtual acoustics and multi-variate analyses to decode room simulations from brain activity during distance perception and identify the auditory factors that drive the pattern of activity in the brain.

neuroscience↗

bioRxiv2024

Macrovascular contributions to resting-state fMRI signals: A comparison between EPI and bSSFP at 9.4 Tesla

The draining-vein bias of T2*-weighted sequences, like gradient echo echo-planar imaging (GRE-EPI), can limit the spatial specificity of functional MRI (fMRI). The underlying extravascular signal changes increase with field strength (B0) and the perpendicularity of draining veins to the main axis of B0, and are therefore particularly problematic at ultra-high field (UHF). In contrast, simulations showed that T2-weighted sequences are less affected by the draining-vein bias, depending on the amount of rephasing of extravascular signal. As large pial veins on the cortical surface follow the cortical folding tightly, their orientation can be approximated by the cortical orientation to [Formula]. In our work, we compare the influence of the cortical orientation to [Formula] on the resting-state fMRI signal of three sequences aiming to understand their macrovascular contribution. While 2D GRE-EPI and 3D GRE-EPI (both T2*-weighted) showed a high dependence on the cortical orientation to [Formula], especially on the cortical surface, this was not the case for 3D balanced steady-state free precession (bSSFP) (T2/T1-weighted). Here, a slight increase of orientation dependence was shown in depths closest to WM. And while orientation dependence decreased with increased distance to the veins for both EPI sequences, no change in orientation dependence was observed in bSSFP. This indicates the low macrovascular contribution to the bSSFP signal, making it a promising sequence for layer fMRI at UHF.

neuroscience↗

bioRxiv2022

Evaluating the capabilities and challenges of layer-fMRI VASO at 3T

Sub-millimeter functional imaging has the potential to capture cortical layer-specific functional information flow within and across brain systems. Recent sequence advancements of fMRI signal readout and contrast generations resulted in wide adaptation of layer-fMRI protocols across the global ultra-high-field (UHF) neuroimaging community. However, most layer-fMRI applications are confined to one of {approx}100 privileged UHF imaging centers, and sequence contrasts with unwanted sensitivity to large draining veins. In this work, we propose the application of vein-signal free vascular space occupancy (VASO) layerfMRI sequences at widely accessible 3T scanners. Specifically, we implement, characterize, and apply a cerebral blood volume (CBV)-sensitive VASO fMRI at a 3T scanner setup, as it is typically used in the majority of cognitive neuroscience and clinical neuroscience fMRI studies. We find that the longer [Formula], and stronger relative T1 contrast at 3T can account for some of the lower z-magnetization in the inversion-recovery VASO sequence compared to 7T and 9.4T. In the main series of experiments (N=16), we test the utility of this setup for motor tasks and find that-while being limited by thermal noise-3T layer-fMRI VASO is feasible within conventional scan durations. In a series of auxiliary studies, we furthermore explore the generalizability of the developed layer-fMRI protocols for a larger range of study designs including: visual stimulation, whole brain movie watching paradigms, and cognitive tasks with weaker effect sizes. We hope that the developed imaging protocols will help to increase accessibility of vein-signal free layer-fMRI imaging tools to a wider community of neuroimaging centers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/501554v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@1b2c6b5org.highwire.dtl.DTLVardef@139b13org.highwire.dtl.DTLVardef@129ff82org.highwire.dtl.DTLVardef@45e9d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Hippocampal subfields and their neocortical interactions during autobiographical memory using submillimeter whole-brain fMRI at 7 Tesla

Advances in ultra-high field 7 Tesla functional magnetic resonance imaging (7T fMRI) have provided unprecedented opportunities to gain insights into the neural underpinnings supporting human memory. The hippocampus, a heterogeneous brain structure comprising several subfields plays a central role during vivid re-experiencing of autobiographical memories (AM). However, due to technical limitations, how hippocampal subfields differentially support AM, whether this contribution is specific to one portion along the hippocampal long-axis, and how subfields are functionally connected with other brain regions typically associated with AM retrieval remains elusive. Here, we leveraged technical advances of parallel imaging and employed a submillimeter Echo Planar Imaging sequence over the whole brain while participants re-experienced vivid, detail-rich AM. We found that all hippocampal subfields along the long-axis were engaged during AM retrieval. Nonetheless, only the pre/parasubiculum within the anterior body of the hippocampus, contributed over and above to AM retrieval. Moreover, whole-brain functional connectivity analyses of the same data revealed that this part of the hippocampus was the only one that was strongly connected to other brain regions typically associated with AM, such as the ventromedial prefrontal cortex (vmPFC) and medial/lateral parietal regions. In the context of the broader literature, our results support recent proposals that the anterior body of the pre/parasubiculum may play an essential role in scene-based cognition, such as the re-experience of personal past events. HighlightsO_LIAll hippocampal subfields differentiate AM retrieval from mental arithmetic problem solving C_LIO_LIThe anterior body of the pre/parasubiculum engages in AM more than other subfields C_LIO_LIThe anterior body of the pre/parasubiculum is strongly connected to the AM network C_LIO_LIThe pre/parasubiculum may be preferentially involved in scene-based cognition C_LI

neuroscience↗

bioRxiv2020

Segmented K-Space Blipped-Controlled Aliasing in Parallel Imaging (Skipped-CAIPI) for High Spatiotemporal Resolution Echo Planar Imaging

PurposeA segmented k-space blipped-CAIPI (skipped-CAIPI) sampling strategy for echo planar imaging (EPI) is proposed, which allows for a flexible choice of EPI factor and phase encode bandwidth independent of the controlled aliasing (CAIPIRINHA) pattern. Theory and MethodsWith previously proposed approaches, exactly two EPI trajectories were possible given a specific CAIPIRINHA pattern: either with slice gradient blips (blipped-CAIPI), or following a shot-selective approach (higher resolution). Recently, interleaved multi-shot segmentation along shot-selective CAIPI trajectories has been applied for high-resolution anatomical imaging. For more flexibility and a broader range of applications, we propose segmentation along any blipped-CAIPI trajectory. Thus, all EPI factors and phase encode bandwidths available with traditional segmented EPI can be combined with controlled aliasing. ResultsTemporal signal-to-noise ratios of moderate-to-high-resolution time series acquisitions at varying undersampling factors demonstrate beneficial sampling alternatives to blipped-CAIPI or shot-selective CAIPI. Rapid high-resolution scans furthermore demonstrate SNR-efficient and motion-robust structural imaging with almost arbitrary EPI factor and minimal noise penalty. ConclusionsSkipped-CAIPI sampling increases protocol flexibility for high spatiotemporal resolution EPI. In terms of signal-to-noise ratio and efficiency, high-resolution functional or structural scans benefit vastly from a free choice of the CAIPIRINHA pattern. Even at moderate resolutions, the independence of sampling pattern, echo time and image matrix size is valuable for optimized functional protocol design. Although demonstrated with 3D-EPI, skipped-CAIPI is also applicable with simultaneous multislice EPI.

neuroscience↗