Biology subjects

Speck, O.

Publications and source records attributed to Speck, O..

15 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↗

bioRxiv2025

Different dopaminergic circuits defined by D2/D3 receptor availablity patterns show structure-specific links to memory in ageing

Cognitive ageing is marked by progressive decline in episodic memory and dopaminergic function, yet the extent to which individual differences in dopaminergic system integrity influence memory under motivational contexts remains unclear. In this study, we investigated how baseline D2/D3 receptor availability (BPND0) in key dopaminergic pathways relates to reward-modulated memory performance in healthy older adults. Thirty-three healthy seniors (aged 64-85) underwent two session concurrent MR-PET imaging with [1F]fallypride involving scene categorisation task with high- and low-motivational contexts. We quantified BPND0 across nine dopaminergic regions of interest and examined their relationships with recognition memory performance at short ([~]15m) and long ([~]24h) delays. Baseline D2/D3 receptor availability showed high test-retest reliability and regionally distinct profiles, suggesting it reflects a stable neurochemical characteristic in healthy ageing, and principal axis factor analysis revealed two partially independent dopaminergic subsystems (dorsal striatal vs mesolimbic) based on interindividual patterns in receptor densities. Region-specific associations further linked D2/D3 receptor availability to distinct memory outcomes. Higher caudate D2/D3 receptor availability was associated with a liberal response bias (increased hits and false alarms both), whereas higher putamen D2/D3 predicted more durable long-term memory retention. Greater thalamic D2/D3 receptor availability correlated with fewer short-term false memories, while greater D2/D3 receptor availability in the amygdala was associated with better recognition at longer delays. In contrast, higher midbrain (substantia nigra and ventral tegmental area) D2/D3 availability which was linked to poorer reward-related memory performance. These findings suggest several complementary dopaminergic circuits supporting episodic memory. Our results highlight dopaminergic neuromodulation as a key factor in cognitive ageing and a potential target for interventions to bolster memory in late life. Patient consent and ethics approvalAll subjects who were included in this study have provided their consent prior to their participation, following the guidelines of the ethics committee at University Hospital Magdeburg in Magdeburg, Germany.

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

Decoding Salience: A Functional Magnetic Resonance Imaging Investigation of Reward and Contextual Unexpectedness in Memory Encoding and Retrieval

The present study investigated the neuromodulatory substrates of salience processing and its impact on memory encoding and behaviour, with a specific focus on two distinct types of salience: reward and contextual unexpectedness. 46 participants performed a novel task paradigm modulating these two aspects independently and allowing for investigating their distinct and interactive effects on memory encoding while undergoing high resolution fMRI. By using advanced image processing techniques tailored to examine midbrain and brainstem nuclei with high precision, our study additionally aimed to elucidate differential activation patterns in subcortical nuclei in response to reward-associated and contextually unexpected stimuli, including distinct pathways involving in particular dopaminergic modulation. We observed a differential involvement of the ventral striatum, substantia nigra and caudate nucleus, as well as a functional specialisation within the subregions of the cingulate cortex for the two salience types. Moreover, distinct subregions within the substantia nigra in processing salience could be identified. Dorsal areas preferentially processed salience related to stimulus processing (of both reward and contextual unexpectedness) versus ventral areas were involved in salience-related memory encoding (for contextual unexpectedness only). These functional specialisations within SN are in line with different projection patterns of dorsal and ventral SN to brain areas supporting attention and memory, respectively. By disentangling stimulus processing and memory encoding related to two salience types, we hope to further consolidate our understanding of neuromodulatory structures differential as well as interactive roles in modulating behavioural responses to salient events.

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

A layer-specific model of cortical sensory aging

The segregation of processes into cortical layers is a convergent feature in animal evolution. However, how changes in the cortical layer architecture interact with sensory system function and dysfunction remains unclear. We conducted functional and structural layer-specific in-vivo 7T-MRI of the primary somatosensory cortex in two cohorts of healthy younger and older adults. Input layer IV is enlarged and more myelinated in older adults, and associated with extended sensory input signals. Age-related cortical thinning is driven by deep layers and accompanied by increased myelination, but there is no clear evidence for reduced inhibition. Calcium imaging and histology in younger and older mice reveal increased sensory-evoked neuronal activity accompanied by increased parvalbumin expression as a potential inhibitory balance, with dynamic changes in layer-specific myelination across age groups. Using multimodal imaging, we demonstrate that middle and deep layers show specific sensitivity to aging across species.

neuroscience↗

bioRxiv2023

Reduced dimension stimulus decoding and column-based modeling reveal architectural differences of primary somatosensory finger maps between younger and older adults

The primary somatosensory cortex (SI) contains fine-grained tactile representations of the body, arranged in an orderly fashion. Using ultra-high resolution fMRI data to describe such detailed individual topographic maps or to detect group differences is challenging, because group alignment often does not preserve the high spatial detail of the data. Here, we use shared response modeling (SRM), a technique that allows group analyses by mapping individual stimulus-driven responses to a lower dimensional shared feature space, to detect age-related differences in sensory representations between younger and older adults using 7T-fMRI data. Using this method, we show that finger representations are more precise in Brodmann-Area (BA) 3b and BA1 compared to BA2 and motor areas, and that this hierarchical processing is preserved across age groups. By combining SRM with column-based decoding (C-SRM), we further show that the number of columns that optimally describes finger maps in SI is higher in younger compared to older adults in BA1, indicating a greater columnar size in older adults SI. Taken together, we conclude that SRM is suitable for finding fine-grained group differences in SI fMRI data at ultra-high-resolution, and we provide first evidence that the columnar architecture of a functional area changes with increasing age.

neuroscience↗

bioRxiv2022

The 3D Structural Architecture of the Human Hand Area is Non-Topographic

The functional topography of the human primary somatosensory cortex (S1) hand area is a widely studied model system to understand sensory organization and plasticity. It is so far unclear whether or not the underlying 3D structural architecture also shows a topographic organization. We used 7T MRI data to quantify layer-specific myelin, iron and mineralization in relation to population receptive field maps of individual finger representations in Brodman area 3b (BA 3b) of human S1 in female and male younger adults. This 3D description allowed us to identify a characteristic profile of layer-specific myelin and iron deposition in the BA 3b hand area, but revealed an absence of structural differences, an absence of low-myelin borders, and high similarity of 3D microstructure profiles between individual fingers. However, structural differences and borders were detected between the hand and face areas. We conclude that the 3D structural architecture of the human hand area is non-topographic, unlike in some monkey species, which suggests a high degree of flexibility for functional finger organization and a new perspective on human topographic plasticity. Significance StatementUsing ultra-high field MRI, we provide the first comprehensive in vivo description of the 3D structural architecture of the human BA 3b hand area in relation to functional population receptive field (pRF) maps. High similarity of precise finger-specific 3D profiles, together with an absence of structural differences and an absence of low-myelin borders between individual fingers, reveal the 3D structural architecture of the human hand area to be non-topographic. This suggests reduced structural limitations to cortical plasticity and reorganization, and allows for shared representational features across fingers.

neuroscience↗

bioRxiv2021

It is the Locus Coeruleus! Or... is it? : A proposition for analyses and reporting standards for structural and functional magnetic resonance imaging of the noradrenergic Locus Coeruleus

The noradrenergic locus coeruleus (LC) in the brainstem shows early signs of protein pathologies in neurodegenerative diseases such as Alzheimers and Parkinsons disease. As the LCs small size (approximately 2.5 mm in width) presents a challenge for molecular imaging, the past decade has seen a steep rise in structural and functional Magnetic Resonance (MR) studies aiming to characterise the LCs changes in ageing and neurodegeneration. However, given its position in the brainstem and small volume, great care must be taken to yield methodologically reliable MR results as spatial deviations in transformations can greatly reduce the statistical power of the analyses at the group level. Here, we suggest a spatial transformation procedure and a set of quality assessment methods which allow LC researchers to achieve the spatial precision necessary for investigating this small but potentially impactful brain structure. Using a combination of available toolboxes (SPM12, ANTs, FSL, FreeSurfer), individual structural and functional 3T LC scans are transformed into MNI space via a study-specific anatomical template. Following this, the precision of spatial alignment in individual MNI-transformed images is quantified using in-plane distance measures based on slice-specific centroids of structural LC segmentations and based on landmarks of salient anatomical features in mean functional images, respectively. Median in-plane distance of all landmarks on the transformed structural as well as functional LC imaging data were below 2 mm, thereby falling below the typical LC width of 2.5 mm suggested by post-mortem data. With the set of spatial post-processing steps outlined in this paper and available for download, we hope to give readers interested in LC imaging a starting point for a reliable analysis of structural and functional MR data of the LC and to have also taken a first step towards establishing reporting standards of LC imaging data.

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↗

bioRxiv2019

Dissociable roles of cortical excitation-inhibition balance during patch-leaving versus value-guided decisions

In a dynamic world, it is essential to decide when to leave an exploited resource. Such patch-leaving decisions involve balancing the cost of moving against the gain expected from the alternative patch. This is in contrast with value-guided decisions that typically involve maximizing reward by selecting the current best option. Patterns of neuronal activity pertaining to patch-leaving decisions have been reported in the dorsal anterior cingulate cortex (dACC), whereas competition via mutual inhibition in the ventromedial prefrontal cortex (vmPFC) is thought to underlie value-guided choice. Here, we show that the balance between cortical excitation and inhibition (E/I balance), measured by the ratio of GABA and glutamate concentrations, plays a dissociable role for the two kinds of decisions. Patch-leaving decision behaviour was related to E/I balance in dACC. In contrast, value-guided decision making was related to E/I balance in vmPFC. These results support previous mechanistic accounts of value-guided choice and provide novel evidence for a role of dACC E/I balance in patch-leaving decisions.

neuroscience↗

bioRxiv2019

Triple visual hemifield maps in optic chiasm hypoplasia

In humans, each hemisphere comprises an overlay of two visuotopic maps of the contralateral visual field, one from each eye. Is the capacity of the visual cortex limited to these two maps or are plastic mechanisms available to host more maps? Using an integrative approach of submillimeter fMRI, diffusion-weighted imaging and population receptive field mapping, we found three hemiretinal inputs to converge onto the left hemisphere in a rare individual with chiasma hypoplasia. This generates extremely atypical responses in striate and extrastriate cortices, specifically an overlay of three hemifield representations. Unexpectedly, the effects of this large abnormality on visual function in daily life are not easily detected. We conclude that developmental plasticity including the re-wiring of local intra- and cortico-cortical connections is pivotal to support the coexistence and functioning of three hemifield maps within one hemisphere.

neuroscience↗

bioRxiv2018

The effect of acquisition resolution on orientation decoding from V1: comparison of 3T and 7T

Previously published results indicate that the accuracy of decoding visual orientation from 7T fMRI data of V1 peaks at spatial acquisition resolutions that are routinely accessible with more conventional 3T scanners. This study directly compares the decoding performance between a 3T and a 7T dataset that were acquired using the same stimulation paradigm by applying an identical analysis procedure. The results indicate that decoding models built on 3T data are comparatively impaired. Moreover, we found no evidence for a strong coupling of BOLD signal change magnitude or temporal signal to noise ratio (tSNR) with decoding performance. Direct enhancement of tSNR via multiband fMRI acquisition at the same resolution did not translate into improved decoding performance. Additional voxel selection can boost 3T decoding performance to the 7T level only at a 3mm acquisition resolution. In both datasets the BOLD signal available for orientation decoding is spatially broadband, but, consistent with the size of the BOLD point-spread-function, decoding models at 3T utilize spatially coarser image components.

neuroscience↗

bioRxiv2016

The effect of acquisition resolution on orientation decoding from V1 BOLD fMRI at 7 Tesla

A decade after it was shown that the orientation of visual grating stimuli can be decoded from human visual cortex activity by means of multivariate pattern classification of BOLD fMRI data, numerous studies have investigated which aspects of neuronal activity are reflected in BOLD response patterns and are accessible for decoding. However, it remains inconclusive what the effect of acquisition resolution on BOLD fMRI decoding analyses is. The present study is the first to provide empirical ultra high-field fMRI data recorded at four spatial resolutions (0.8 mm, 1.4 mm, 2 mm, and 3 mm isotropic voxel size) on this topic -- in order to test hypotheses on the strength and spatial scale of orientation discriminating signals. We present detailed analysis, in line with predictions from previous simulation studies, about how the performance of orientation decoding varies with different acquisition resolutions. Moreover, we also examine different spatial filtering procedures and its effects on orientation decoding. Here we show that higher-resolution scans with subsequent down-sampling or low-pass filtering yield no benefit over scans natively recorded in the corresponding lower resolution regarding decoding accuracy. The orientation-related signal in the BOLD fMRI data is spatially broadband in nature, includes both high spatial frequency components, as well as large-scale biases previously proposed in the literature. Moreover, we found above chance-level contribution from large draining veins to orientation decoding. Acquired raw data were publicly released to facilitate further investigation.

neuroscience↗