Biology subjects

Mattern, H.

Publications and source records attributed to Mattern, H..

10 recordsLinked to original sources

bioRxiv2026

Field-Correcting GRAPPA (FCG): a technique to correctspatiotemporal-varying phase errors in Echo Planar Imaging

PurposeTo develop a Field-Correcting GRAPPA (FCG) technique to correct the spatiotemporal-varying phase errors in EPI caused by eddy currents. MethodsThe fast-changing gradient in EPI causes strong eddy current effects and associated spatiotemporal-varying phase errors, producing significant image artifacts. The use of higher gradient amplitude, slew rate, and ramp sampling factor for faster imaging exacerbates this problem. In this work, FCG was developed to address this challenge by using a multi-layer perceptron (MLP) to provide a compact representation of a family of GRAPPA-like kernels that correct the spatiotemporal-varying phase errors in the data. A dedicated calibration pipeline was designed to acquire high-quality source and target data for MLP training in both slice-by-slice and simultaneous multi-slice (SMS) acquisitions. To validate FCGs assumptions and performance, a field camera was used to provide ground-truth measurement of phase patterns. The performance of FCG was further validated on phantom and in vivo experiments using demanding EPI trajectories across multiple 3T and 7T systems. ResultsField camera measurements revealed strong spatiotemporal phase variations along the kx direction that repeat along ky during EPI readouts. The experiments on high-performance systems across 3T and 7T demonstrate that FCG can provide superior correction for the artifacts induced by spatiotemporal-varying phase errors compared with existing approaches. ConclusionFCG is an effective and robust method for correcting spatiotemporal phase errors in EPI, enabling improved image quality on high-performance systems.

bioengineering↗

bioRxiv2026

The in-vivo microstructural profile of human hippocampal subfield CA1 and its relation to memory performance

The hippocampal CA1 subregion supports learning, memory formation, and spatial navigation. Although its three-layered architecture has been described in ex-vivo investigations, the in-vivo microstructural profile of CA1 and its relation to individual variations in memory performance remain poorly characterized. In this study, we used ultra-high field structural MRI at 7 Tesla to investigate the depth-dependent myelination patterns (measured by quantitative T1) of CA1 in younger adults, their relation to the local arterial architecture, and their association with individual differences in cognitive functions, specifically memory performance. Results show that left and right CA1 present depth-dependent patterns of myelination, with the outer and inner compartments showing higher myelination than the middle compartment. No significant relationship between layer-specific myelination of CA1 and distance to the nearest artery was observed. Right CA1 was found to be more myelinated than left CA1. Pairwise correlations and regression models showed that higher left CA1 myelination is linked to higher accuracy in object localization. Together, our data demonstrates the feasibility of describing the three layered myelin architecture of CA1 in vivo, and provides information on how alterations in the architecture of CA1 may relate to alterations in cognitive performance in younger adults.

neuroscience↗

bioRxiv2025

Modeling 2D Spatio-Tactile Population Receptive Fields of the Fingertip in Human Primary Somatosensory Cortex

Tactile fingertip sensations are critical for everyday life. Accordingly, tactile fingertip maps have been extensively studied in human primary somatosensory cortex. However, the fine-grained functional architecture of these maps remains largely unknown. To uncover this architecture, we sought to estimate 2D spatio-tactile population receptive fields (pRFs) of the tip of the index finger in human Brodmann area 3b (BA3b). Using functional magnetic resonance imaging at 7T and submillimeter resolution along with prospective motion correction, we recorded brain responses whilst participants sensed a row of vibrotactile pins sweeping along cardinal axes over a portion of the fingertip. To estimate pRF position and size, we initially fit a 2D Gaussian pRF model to the data, which, however, produced largely implausible pRF estimates. Simulations indicated that this likely occurred because the size of pRFs in BA3b surpasses the portion of the fingertip we stimulated, resulting in an incomplete mapping of pRFs. To address this issue, we constrained the fitting procedure and refined the 2D Gaussian pRF model by keeping pRF size constant. Our results for pRF position then revealed that the ulnar-to-radial axis spanning the fingertip maps onto a superior-to-inferior axis in BA3b. Both the putatively large pRF size (relative to the mapping area) and the pRF position gradient we uncover here appear compatible with receptive field properties quantified in monkeys. Our study provides the first comprehensive investigation into the fine-grained functional architecture of human fingertip maps and brings us one step closer to a thorough understanding thereof.

neuroscience↗

bioRxiv2025

Individualized Phenotyping of Functional ALS Pathology in Sensorimotor Cortex

Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease characterized by the loss of motor neurons in primary motor cortex (MI), leading to muscle weakness, atrophy, and death within a median of three years. Even though ALS is characterized by different disease subtypes affecting different body parts, individiualized phenotyping of functional ALS pathology has so far not been achieved. We recorded 7 Tesla functional MRI (7T-fMRI) data while ALS patients and matched controls moved affected and non-affected body parts in the MR scanner. We applied robust Shared Response Modeling (rSRM) for capturing ALS-specific shared responses for group classification, and Partial Least Squares (PLS) regression for relating the latent variables to clinical subtypes and the degree of disease progression. We show that both functional connectivity and functional activation in MI are a predictor for disease onset site. However, disease severity could best be predicted by functional connectivity rather than pure activation changes. Critically, we show that functionally disease-defining information in MI is not strongest in the area that is behaviorally first-affected, deviating from the behavioral phenotype of the patients. When computing the models weight distribution of the King stage classification and projecting them back into voxel space, the highest mean weights are present in the foot and tongue/face regions that seem to drive disease progress. Our data highlight the importance of 7T-fMRI task-based functional connectivity measures for classifying ALS-patients, and provide evidence that a single 7T-MRI scan can be used for identifying a disease signature of each individual ALS patient.

neuroscience↗

bioRxiv2024

VesselBoost: A Python Toolbox for Small Blood Vessel Segmentation in Human Magnetic Resonance Angiography Data

Magnetic resonance angiography (MRA) performed at ultra-high magnetic field provides a unique opportunity to study the arteries of the living human brain at the mesoscopic level. From this, we can gain new insights into the brains blood supply and vascular disease affecting small vessels. However, for quantitative characterization and precise representation of human angioarchitecture to, for example, inform blood-flow simulations, detailed segmentations of the smallest vessels are required. Given the success of deep learning-based methods in many segmentation tasks, we here explore their application to high-resolution MRA data, and address the difficulty of obtaining large data sets of correctly and comprehensively labelled data. We introduce VesselBoost, a vessel segmentation package, which utilizes deep learning and imperfect training labels for accurate vasculature segmentation. Combined with an innovative data augmentation technique, which leverages the resemblance of vascular structures, VesselBoost enables detailed vascular segmentations.

neuroscience↗

bioRxiv2023

Age-Related Differences in Human Cortical Microstructure Depend on the Distance to the Nearest Vein

Age-related differences in cortical microstructure are used to understand the neuronal mechanisms that underlie human brain ageing. The cerebral vasculature contributes to cortical ageing, but its precise interaction with cortical microstructure is poorly understood. In a cross-sectional study, we combine venous imaging with vessel distance mapping (VDM) to investigate the interaction between venous distances and age-related differences in the microstructural architecture of the primary somatosensory cortex (S1), the primary motor cortex (M1), and additional areas in frontal cortex as non-sensorimotor control regions. We scanned 18 younger adults and 17 older adults using 7T-MRI to measure age-related changes in quantitative T1 (qT1) values, positive QSM (pQSM) values, and negative QSM (nQSM) values at 0.5 mm isotropic resolution. We modelled different cortical depths using an equi-volume approach and assessed the distance of each voxel to its nearest vein using VDM. Our data reveal a dependence of cortical qT1 and pQSM values on venous distance. In addition, there is an interaction between venous distance and age on qT1 values, driven by lower qT1 values in older compared to younger adults in voxels that are closer to a vein. Together, our data show that the local venous architecture explains a significant amount of variance in standard measures of cortical microstructure and should be considered in neurobiological models of human brain organisation and cortical ageing.

neuroscience↗

bioRxiv2023

Spatio-temporal dynamics of microglia phenotype in human and murine cSVD: impact of acute and chronic hypertensive states

Vascular risk factors such as chronic hypertension are well established major modifiable factors for the development of cerebral small vessel disease (cSVD). In the present study, our focus was the investigation of cSVD-related phenotypic changes in microglia in human disease and in the spontaneously hypertensive stroke-prone rat (SHRSP) model of cSVD. Our examination of cortical microglia in human post-mortem cSVD cortical tissue revealed distinct morphological microglial features specific to cSVD. We identified enlarged somata, an increase in the territory occupied by thickened microglial processes, and an expansion in the number of vascular-associated microglia. In parallel, we characterized microglia in a rodent model of hypertensive cSVD along different durations of arterial hypertension, i.e., early chronic and late chronic hypertension. Microglial somata were already enlarged in early hypertension, whereas at late-stage chronic hypertension they further exhibited elongat ed branches, thickened processes, and a reduced ramification index, mirroring the findings in human cSVD. An unbiased multidimensional flow cytometric analysis revealed phenotypic heterogeneit y among microglia cells within the hippocampus and cortex. At early-stage hypertension, hippocampal microglia exhibited upregulated CD11b/c, P2Y12R, CD200R, and CD86 surface markers. Detailed analysis of cell subpopulations revealed a unique microglial subset expressing CD11b/c, CD163, and CD86 exclusively in early hypertension. Notably, even at early-stage hypertension, microglia displayed a higher association with cerebral blood vessels. We identified several profound clusters of microglia expressing distinct marker profiles at late chronic hypertensive states. We further detected a temporal hypertension-related disturbances in blood-brain barrier integrity, accompanied by increased recruitment of leukocytes to the brain parenchyma in early hypertension. In summary, our findings demonstrate a higher vulnerability of the hippocampus, stage-specific microglial signatures based on morphological features, and cell surface protein expression in response to chronic arterial hypertension. These results indicate the diversity within microglia sub-populations and implicate the subtle involvement of microglia in cSVD pathogenesis.

neuroscience↗

bioRxiv2023

Vascular and neural transcriptomics reveal stage-dependent pathways to inflammation and cognitive dysfunction in a rat model of hypertension

Chronic arterial hypertension causes cerebral microvascular dysfunction and doubles dementia risk in aging. However, cognitive health preservation by therapeutic blood pressure lowering alone is limited and depends on disease duration, the degree of irreversible tissue damage and whether microvascular function can be restored. This study aimed to understand molecular and cellular temporo-spatial pathomechanisms in the course of hypertension. We investigated the effects of initial, early chronic and late chronic hypertension in the frontal brain of rats by applying behavioral tests, histopathology, immunofluorescence, FACS, microvascular/neural tissue RNA sequencing as well as 18F-FDG PET imaging. Chronic hypertension caused frontal brain-specific behavioral deficits. Our results highlight stage-dependent responses to continuous microvascular stress and wounding by hypertension. Early responses included a fast recruitment of activated microglia to the blood vessels, immigration of peripheral immune cells, blood-brain-barrier leakage and an energy-demanding hypermetabolic state. Vascular adaptation mechanisms were observed in later stages and included angiogenesis and vessel wall strengthening by upregulation of cellular adhesion molecules and extracellular matrix. Additionally, we identified late chronic accumulation of Igfbp-5 in the brains of hypertensive rats, which is also a signature of Alzheimers dementia and attenuates protective Igf-1 signaling. Our study advances the knowledge of involved pathomechanisms and highlights the stage-dependent nature of hypertensive pathobiology. This groundwork might be helpful for basic and clinical research to identify stage-dependent markers in the human disease course, investigate stage-dependent interventions besides blood pressure lowering and better understand the relationship between poor vascular health and neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Imaging of the pial arterial vasculature of the human brain in vivo using high-resolution 7T time-of-flight angiography

The pial arterial vasculature of the human brain is the only blood supply to the neocortex, but quantitative data on the morphology and topology of these mesoscopic arteries (diameter 50- 300 {micro}m) remains scarce. Because it is commonly assumed that blood flow velocities in these vessels are prohibitively slow, non-invasive time-of-flight MRI angiography (TOF-MRA)--which is well-suited to high 3D imaging resolutions--has not been applied to imaging the pial arteries. Here, we provide a theoretical framework that outlines how TOF-MRA can visualize small pial arteries in vivo, by employing extremely small voxels at the size of individual vessels. We then provide evidence for this theory by imaging the pial arteries at 140-{micro}m isotropic resolution using a 7T MRI scanner and prospective motion correction, and show that pial arteries one voxel-width in diameter can be detected. We conclude that imaging pial arteries is not limited by slow blood flow, but instead by achievable image resolution. This study represents the first targeted, comprehensive account of imaging pial arteries in vivo in the human brain. This ultra-high-resolution angiography will enable the characterization of pial vascular anatomy across the brain to investigate patterns of blood supply and relationships between vascular and functional architecture.

neuroscience↗

bioRxiv2021

Perceived and mentally rotated contents are differentially represented in cortical depth of V1

Primary visual cortex (V1) in humans is known to represent both veridically perceived external input and internally-generated contents underlying imagery and mental rotation. However, it is unknown how the brain keeps these contents separate thus avoiding a mixture of the perceived and the imagined which could lead to potentially detrimental consequences. Inspired by neuroanatomical studies showing that feedforward and feedback connections in V1 terminate in different cortical layers, we hypothesized that this anatomical compartmentalization underlies functional segregation of external and internally-generated visual contents, respectively. We used high-resolution layer-specific fMRI to test this hypothesis in a mental rotation task. We found that rotated contents were predominant at outer cortical depth bins (i.e. superficial and deep). At the same time perceived contents were represented stronger at the middle cortical bin. These results identify how through cortical depth compartmentalization V1 functionally segregates rather than confuses external from internally-generated visual contents. These results indicate that feedforward and feedback manifest in distinct subdivisions of the early visual cortex, thereby reflecting a general strategy for implementing multiple cognitive functions within a single brain region.

neuroscience↗