wmh_seg: Transformer based U-Net for Robust and Automatic White Matter Hyperintensity Segmentation across 1.5T, 3T and 7T

White matter hyperintensity (WMH) remains the top imaging biomarker for neurodegenerative diseases. Robust and accurate segmentation of WMH holds paramount significance for neuroimaging studies. The growing shift from 3T to 7T MRI necessitates robust tools for harmonized segmentation across field strengths and artifacts. Recent deep learning models exhibit promise in WMH segmentation but still face challenges, including diverse training data representation and limited analysis of MRI artifacts' impact. To address these, we introduce wmh_seg, a novel deep learning model leveraging a transformer-based encoder from SegFormer. wmh_seg is trained on an unmatched dataset, including 1.5T, 3T, and 7T FLAIR images from various sources, alongside with artificially added MR artifacts. Our approach bridges gaps in training diversity and artifact analysis. Our model demonstrated stable performance across magnetic field strengths, scanner manufacturers, and common MR imaging artifacts. Despite the unique inhomogeneity artifacts on ultra-high field MR images, our model still offers robust and stable segmentation on 7T FLAIR images. Our model, to date, is the first that offers quality white matter lesion segmentation on 7T FLAIR images

Single subject and group whole-brain fMRI mapping of male genital sensation at 7 Tesla

Processing of genital sensations in the central nervous system of humans is still poorly understood. Current knowledge is mainly based on neuroimaging studies using electroencephalography (EEG), magneto-encephalography (MEG), and 1.5- or 3- Tesla (T) functional magnetic resonance imaging (fMRI), all of which suffer from limited spatial resolution and sensitivity, thereby relying on group analyses to reveal significant data. Here, we studied the impact of passive, yet non-arousing, tactile stimulation o

The Role of the Striatum in Learning to Orthogonalize CD Action and Valence: A Combined PET and 7 T MRI Aging Study

Pavlovian biases influence instrumental learning by coupling reward seeking with action invigoration and punishment avoidance with action suppression. Using a probabilistic go/no-go task designed to orthogonalize action (go/no-go) and valence (reward/punishment), recent studies have shown that the interaction between the two is dependent on the striatum and its key neuromodulator dopamine. Using this task, we sought to identify how structural and neuromodulatory age-related differences in the striatum may influence Pavlovian biases and instrumental learning in 25 young and 31 older adults. Computational modeling revealed a significant age-related reduction in reward and punishment sensitivity and marked (albeit not significant) reduction in learning rate and lapse rate (irreducible noise). Voxel-based morphometry analysis using 7 Tesla MRI images showed that individual differences in learning rate in older adults were related to the volume of the caudate nucleus. In contrast, dopamine synthesis capacity in the dorsal striatum, assessed using [18F]-DOPA positron emission tomography in 22 of these older adults, was not associated with learning performance and did not moderate the relationship between caudate volume and learning rate. This multiparametric approach suggests that age-related differences in striatal volume may influence learning proficiency in old age

Neurobiological and metabolic mechanisms of binge-eating in anorexia and bulimia nervosa

Binge-eating is characterised by the recurrent consumption of large amounts of food, which co-occurs with a subjective loss of control over intake. This transdiagnostic syndrome results in significant distress, functional impairment and comorbidity. However, precise characterisation of the physiological and neurobiological mechanisms that give rise to, or maintain, this behaviour is lacking. This thesis integrates observations across metabolic, neural and behavioural levels in women with and without eating disorders, providing novel insights into how perturbations across each strata interact with one another in illness and in health to shape eating behaviour. In Chapter 1, I review the classification of binge-eating disorders prior to summarising the extant literature on homeostatic and non-homeostatic mechanisms that influence (ab)normal eating behaviour. This introductory chapter also reviews current perspectives on how psychological stress influences disordered eating, outlining the motivation for the multimodal neuroimaging protocol detailed in Chapter 2. Chapter 2 focuses on the specific methodology of this neuroimaging study, which examined the impact of acute, psychological stress on gut hormones, endocrine responses, and inhibitory control in women acutely ill with the binge-eating and purging subtype of anorexia nervosa, bulimia nervosa and matched controls. Chapters 3 through 5 report the results of this study. Chapter 3 focuses on findings of dissociable hormonal responses to stress in anorexia and bulimia nervosa, presenting novel evidence that links acute changes in mental state to altered gut hormone signalling in anorexia nervosa. Chapter 4 is dedicated to the functional magnetic resonance imaging arm of the protocol, which rigorously examined the impact of diagnosis and induced stress on two forms of response inhibition: proactive and reactive control. Chapter 5 provides insight into associations between peripheral metabolic markers and neural integrity of the cerebral cortex in patients and controls. Finally, Chapter 6 provides a brief summary, discusses the implications of these findings and presents some ongoing and future research that extends this original work. In summary, this thesis represents, to my knowledge, the first attempt to generate a multi-level framework for understanding the physiological and psychological mechanisms of illnesses characterised by binge-eating. Findings identify important metabolic and neurobiological distinctions between two eating disorders with shared symptomatology, demonstrating the need for, and value in, integrative models of mental illness.Cambridge International Trust; NIH Oxford Cambridge Scholars Progra

Imaging the subthalamic nucleus in Parkinson’s disease

This thesis is comprised of a set of work that aims to visualize and quantify the anatomy, structural variability, and connectivity of the subthalamic nucleus (STN) with optimized neuroimaging methods. The study populations include both healthy cohorts and individuals living with Parkinson's disease (PD). PD was chosen specifically due to the involvement of the STN in the pathophysiology of the disease. Optimized neuroimaging methods were primarily obtained using ultra-high field (UHF) magnetic resonance imaging (MRI). An additional component of this thesis was to determine to what extent UHF-MRI can be used in a clinical setting, specifically for pre-operative planning of deep brain stimulation (DBS) of the STN for patients with advanced PD. The thesis collectively demonstrates that i, MRI research, and clinical applications must account for the different anatomical and structural changes that occur in the STN with both age and PD. ii, Anatomical connections involved in preparatory motor control, response inhibition, and decision-making may be compromised in PD. iii. The accuracy of visualizing and quantifying the STN strongly depends on the type of MR contrast and voxel size. iv, MRI at a field strength of 3 Tesla (T) can under certain circumstances be optimized to produce results similar to that of 7 T at the expense of increased acquisition time

Bladder Dysfunction in the Context of the Bladder-Brain Connection

The aim of the thesis "Bladder dysfunction in the context of the bladder-brain connection" written by Ilse Groenendijk, was to investigate potential diagnostic tools in the field of functional urology. The first aim was to define the brain areas involved in LUT control in healthy individuals and to investigate the clinical applicability of dynamic brain imaging as a diagnostic tool of functional bladder disorders in individuals. The second aim was to evaluate and improve traditional and patient reported outcome measurements in the field of functional urology