Improving the clinico-radiological association in neurological diseases

Despite the key role of magnetic resonance imaging (MRI) in the diagnosis and monitoring of multiple sclerosis (MS) and cerebral small vessel disease (SVD), the association between clinical and radiological disease manifestations is often only moderate, limiting the use of MRI-derived markers in the clinical routine or as endpoints in clinical trials. In the projects conducted as part of this thesis, we addressed this clinico-radiological gap using two different approaches. Lesion-symptom association: In two voxel-based lesion-symptom mapping studies, we aimed at strengthening lesion-symptom associations by identifying strategic lesion locations. Lesion mapping was performed in two large cohorts: a dataset of 2348 relapsing-remitting MS patients, and a population-based cohort of 1017 elderly subjects. T2-weighted lesion masks were anatomically aligned and a voxel-based statistical approach to relate lesion location to different clinical rating scales was implemented. In the MS lesion mapping, significant associations between white matter (WM) lesion location and several clinical scores were found in periventricular areas. Such lesion clusters appear to be associated with impairment of different physical and cognitive abilities, probably because they affect commissural and long projection fibers. In the SVD lesion mapping, the same WM fibers and the caudate nucleus were identified to significantly relate to the subjects’ cerebrovascular risk profiles, while no other locations were found to be associated with cognitive impairment. Atrophy-symptom association: With the construction of an anatomical physical phantom, we aimed at addressing reliability and robustness of atrophy-symptom associations through the provision of a “ground truth” for atrophy quantification. The built phantom prototype is composed of agar gels doped with MRI and computed tomography (CT) contrast agents, which realistically mimic T1 relaxation times of WM and grey matter (GM) and showing distinguishable attenuation coefficients using CT. Moreover, due to the design of anatomically simulated molds, both WM and GM are characterized by shapes comparable to the human counterpart. In a proof-of-principle study, the designed phantom was used to validate automatic brain tissue quantification by two popular software tools, where “ground truth” volumes were derived from high-resolution CT scans. In general, results from the same software yielded reliable and robust results across scans, while results across software were highly variable reaching volume differences of up to 8%

Power in Voxel-based Lesion–Symptom Mapping

Lesion analysis in brain-injured populations complements what can be learned from functional neuroimaging. Voxelbased approaches to mapping lesion–behavior correlations in brain-injured populations are increasingly popular, and have the potential to leverage image analysis methods drawn from functional magnetic resonance imaging. However, power is a major concern for these studies, and is likely to vary regionally due to the distribution of lesion locations. Here, we outline general considerations for voxel-based methods, characterize the use of a nonparametric permutation test adapted from functional neuroimaging, and present methods for regional power analysis in lesion studies

Large-scale inference in the focally damaged human brain

Clinical outcomes in focal brain injury reflect the interactions between two distinct anatomically distributed patterns: the functional organisation of the brain and the structural distribution of injury. The challenge of understanding the functional architecture of the brain is familiar; that of understanding the lesion architecture is barely acknowledged. Yet, models of the functional consequences of focal injury are critically dependent on our knowledge of both. The studies described in this thesis seek to show how machine learning-enabled high-dimensional multivariate analysis powered by large-scale data can enhance our ability to model the relation between focal brain injury and clinical outcomes across an array of modelling applications. All studies are conducted on internationally the largest available set of MR imaging data of focal brain injury in the context of acute stroke (N=1333) and employ kernel machines at the principal modelling architecture. First, I examine lesion-deficit prediction, quantifying the ceiling on achievable predictive fidelity for high-dimensional and low-dimensional models, demonstrating the former to be substantially higher than the latter. Second, I determine the marginal value of adding unlabelled imaging data to predictive models within a semi-supervised framework, quantifying the benefit of assembling unlabelled collections of clinical imaging. Third, I compare high- and low-dimensional approaches to modelling response to therapy in two contexts: quantifying the effect of treatment at the population level (therapeutic inference) and predicting the optimal treatment in an individual patient (prescriptive inference). I demonstrate the superiority of the high-dimensional approach in both settings

Towards a Novel Way to Predict Deficits After a Brain Lesion: A Stroke Example

Many studies have addressed the relations between different human brain regions and their role in cognitive, motor and sensory functions in patients that have suffered a brain lesion (stroke, traumatic brain injury, tissue removal). Nowadays, it is well established that the brain works as a network and the symptoms in a person are a combination of the direct impact of the lesion in a single region and its connectivity with other healthy brain regions. The aim of the present study is the development of a user-friendly desktop application to predict the induced cognitive deficits in patients who have suffered a brain lesion. The herein presented application is based on Neurosynth platform, and takes as an input a MRI mask that describes a lesion. Then our software exploits the knowledge that already exists in Neurosynth platform, so as to predict the potential deficits by grouping the Neurosynth's terms that have increased Z scores with our mask. In addition, we have embedded two types of visualization methods: One to present the slices of the brain mask and another to show the 3D volume of the mask into 3D semitransparent human brain. The added value of the presented application is that it may give us a clue about which mechanisms are probably affected by a lesion in a specific region, while in the future it could provide neurosurgeons with insightful knowledge helping them in the plannification of a forthcoming surgical procedure. The proposed software was tested on 7 stroke patients, predicting accurately the 91% of the measured deficits found during a neuropsychological assessment

Improving Patch-Based Convolutional Neural Networks for MRI Brain Tumor Segmentation by Leveraging Location Information.

The manual brain tumor annotation process is time consuming and resource consuming, therefore, an automated and accurate brain tumor segmentation tool is greatly in demand. In this paper, we introduce a novel method to integrate location information with the state-of-the-art patch-based neural networks for brain tumor segmentation. This is motivated by the observation that lesions are not uniformly distributed across different brain parcellation regions and that a locality-sensitive segmentation is likely to obtain better segmentation accuracy. Toward this, we use an existing brain parcellation atlas in the Montreal Neurological Institute (MNI) space and map this atlas to the individual subject data. This mapped atlas in the subject data space is integrated with structural Magnetic Resonance (MR) imaging data, and patch-based neural networks, including 3D U-Net and DeepMedic, are trained to classify the different brain lesions. Multiple state-of-the-art neural networks are trained and integrated with XGBoost fusion in the proposed two-level ensemble method. The first level reduces the uncertainty of the same type of models with different seed initializations, and the second level leverages the advantages of different types of neural network models. The proposed location information fusion method improves the segmentation performance of state-of-the-art networks including 3D U-Net and DeepMedic. Our proposed ensemble also achieves better segmentation performance compared to the state-of-the-art networks in BraTS 2017 and rivals state-of-the-art networks in BraTS 2018. Detailed results are provided on the public multimodal brain tumor segmentation (BraTS) benchmarks

Diagnosing Alzheimer's Disease using Early-Late Multimodal Data Fusion with Jacobian Maps

Alzheimer's disease (AD) is a prevalent and debilitating neurodegenerative disorder impacting a large aging population. Detecting AD in all its presymptomatic and symptomatic stages is crucial for early intervention and treatment. An active research direction is to explore machine learning methods that harness multimodal data fusion to outperform human inspection of medical scans. However, existing multimodal fusion models have limitations, including redundant computation, complex architecture, and simplistic handling of missing data. Moreover, the preprocessing pipelines of medical scans remain inadequately detailed and are seldom optimized for individual subjects. In this paper, we propose an efficient early-late fusion (ELF) approach, which leverages a convolutional neural network for automated feature extraction and random forests for their competitive performance on small datasets. Additionally, we introduce a robust preprocessing pipeline that adapts to the unique characteristics of individual subjects and makes use of whole brain images rather than slices or patches. Moreover, to tackle the challenge of detecting subtle changes in brain volume, we transform images into the Jacobian domain (JD) to enhance both accuracy and robustness in our classification. Using MRI and CT images from the OASIS-3 dataset, our experiments demonstrate the effectiveness of the ELF approach in classifying AD into four stages with an accuracy of 97.19%.Comment: To be published in Proceedings of 2023 IEEE Healthcom, December 202

Lead-DBS v3.0: Mapping Deep Brain Stimulation Effects to Local Anatomy and Global Networks.

Following its introduction in 2014 and with support of a broad international community, the open-source toolbox Lead-DBS has evolved into a comprehensive neuroimaging platform dedicated to localizing, reconstructing, and visualizing electrodes implanted in the human brain, in the context of deep brain stimulation (DBS) and epilepsy monitoring. Expanding clinical indications for DBS, increasing availability of related research tools, and a growing community of clinician-scientist researchers, however, have led to an ongoing need to maintain, update, and standardize the codebase of Lead-DBS. Major development efforts of the platform in recent years have now yielded an end-to-end solution for DBS-based neuroimaging analysis allowing comprehensive image preprocessing, lead localization, stimulation volume modeling, and statistical analysis within a single tool. The aim of the present manuscript is to introduce fundamental additions to the Lead-DBS pipeline including a deformation warpfield editor and novel algorithms for electrode localization. Furthermore, we introduce a total of three comprehensive tools to map DBS effects to local, tract- and brain network-levels. These updates are demonstrated using a single patient example (for subject-level analysis), as well as a retrospective cohort of 51 Parkinson's disease patients who underwent DBS of the subthalamic nucleus (for group-level analysis). Their applicability is further demonstrated by comparing the various methodological choices and the amount of explained variance in clinical outcomes across analysis streams. Finally, based on an increasing need to standardize folder and file naming specifications across research groups in neuroscience, we introduce the brain imaging data structure (BIDS) derivative standard for Lead-DBS. Thus, this multi-institutional collaborative effort represents an important stage in the evolution of a comprehensive, open-source pipeline for DBS imaging and connectomics

Clinical presentation and neural correlates of stroke‐associated spatial delusions

© 2022 The Authors. European Journal of Neurology published by John Wiley & Sons Ltd on behalf of European Academy of Neurology. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.Background and purpose: Incongruent beliefs about self-localization in space markedly disturb patients' behavior. Spatial delusions, or reduplicative paramnesias, are characterized by a firm conviction of place reduplication, transformation, or mislocation. Evidence suggests they are frequent after right hemisphere lesions, but comprehensive information about their clinical features is lacking. Methods: We prospectively screened 504 acute right-hemisphere stroke patients for the presence of spatial delusions. Their behavioral and clinical features were systematically assessed. Then, we analyzed the correlation of their duration with the magnitude of structural disruption of belief-associated functional networks. Finally, we described the syndrome subtypes and evaluated whether the clinical categorization would be predicted by the structural disruption of familiarity-associated functional networks using an unsupervised k-means clustering algorithm. Results: Sixty patients with spatial delusions were identified and fully characterized. Most (93%) localized the misidentified places closer to home than the hospital. The median time duration was 3 days (interquartile range = 1-7 days), and it was moderately correlated with the magnitude of structural-functional decoupling of belief-associated functional networks (r = 0.39, p = 0.02; beta coefficient regressing for lesion volume = 3.18, p = 0.04). Each clinical subtype had characteristic response patterns, which were reported, and representative examples were provided. Clustering based on structural disruption of familiarity- and unfamiliarity-associated functional networks poorly matched the clinical categorization (lesion: Rand index = 0.47; structural disconnection: Rand index = 0.51). Conclusions: The systematic characterization of the peculiar clinical features of stroke-associated spatial delusions may improve the syndrome diagnosis and clinical approaches. The novel evidence about their neural correlates fosters the clarification of the pathophysiology of delusional misidentifications.This work was supported by the following grants: PRÉMIO JOÃO LOBO ANTUNES 2018–SCML and Bolsa de Investigação em Doenças Vasculares Cerebrais 2017–SPAVC.info:eu-repo/semantics/publishedVersio