Intraoperative Localization of Subthalamic Nucleus during Deep Brain Stimulation Surgery using Machine Learning Algorithms

This thesis presents a novel technique for localizing the Subthalamic Nucleus (STN) during Deep Brain Stimulation (DBS) surgery. DBS is an accepted treatment for individuals living with Parkinson\u27s Disease (PD). This surgery involves implantation of a permanent electrode inside the STN to deliver electrical current. The STN is a small grey matter structure within the brain, which makes accurate placement a challenging task for the surgical team. Prior to placement of the permanent electrode, intraoperative microelectrode recordings (MERs) of neural activity are used to localize the STN. The placement of the permanent electrode and the success of the stimulation therapy depend on accurate localization. In this study, an objective approach was implemented to help the surgical team in localizing the STN. This is achieved by processing the MER signals and extracting features during the surgery to be used in a Machine Learning algorithm for defining the electrophysiological borders of the STN. A classification approach that can detect the borders of the STN during the operation is proposed. MER signals from 100 PD patients were recorded and used to validate the performance of the proposed method. The results show that by extracting wavelet transformation features from MER signals and using a deep neural network architecture, it is possible to detect the border of the STN with an accuracy of 92%. The proposed method can be implemented in real-time during the surgery to assist the surgical team with the goal of enhancing the accuracy and consistency of electrode placement in the STN

Mapping of subthalamic nucleus using microelectrode recordings during deep brain stimulation

Alongside stereotactic magnetic resonance imaging, microelectrode recording (MER) is frequently used during the deep brain stimulation (DBS) surgery for optimal target localization. The aim of this study is to optimize subthalamic nucleus (STN) mapping using MER analytical patterns. 16 patients underwent bilateral STN-DBS. MER was performed simultaneously for 5 microelectrodes in a setting of Ben's-gun pattern in awake patients. Using spikes and background activity several different parameters and their spectral estimates in various frequency bands including low frequency (2-7 Hz), Alpha (8-12 Hz), Beta (sub-divided as Low_Beta (13-20 Hz) and High_Beta (21-30 Hz)) and Gamma (31 to 49 Hz) were computed. The optimal STN lead placement with the most optimal clinical effect/ side-effect ratio accorded to the maximum spike rate in 85% of the implantation. Mean amplitude of background activity in the low beta frequency range was corresponding to right depth in 85% and right location in 94% of the implantation respectively. MER can be used for STN mapping and intraoperative decisions for the implantation of DBS electrode leads with a high accuracy. Spiking and background activity in the beta range are the most promising independent parameters for the delimitation of the proper anatomical site

Caracterización beta, gamma y de oscilaciones de alta frecuencia para localización de diana en procedimientos de Estimulación Cerebral Profunda

Deep Brain Stimulation (DBS) has been successfully used to treat patients with Parkinson’s Disease. DBS employs an electrode that regulates the oscillatory activity of the basal ganglia, such as the subthalamic nucleus (STN). A critical point during the surgical implantation of such electrode is the precise localization of the target. This is done using presurgical images, stereotactic frames, and microelectrode recordings (MER). The latter allows neurophysiologists to visualize the electrical activity of different structures along the surgical track, each of them with well-defined variations in the frequency pattern; however, this is far from an automatic or semi-automatic method to help these specialists make decisions concerning the surgical target. To pave the way to automation, we analyzed three frequency bands in MER signals acquired from 11 patients undergoing DBS: beta (13-40 Hz), gamma (40-200 Hz), and high-frequency oscillations (HFO – 201-400 Hz). In this study, we propose and assess five indexes in order to detect the STN: variations in autoregressive parameters and their derivative along the surgical track, the energy of each band calculated using the Yule-Walker power spectral density, the high-to-low (H/L) ratio, and its derivative. We found that the derivative of one parameter of the beta band and the H/L ratio of the HFO/gamma bands produced errors in STN targeting like those reported in the literature produced by image-based methods (<2 mm). Although the indexes introduced here are simple to compute and could be applied in real time, further studies must be conducted to be able to generalize their results.La estimulación cerebral profunda (DBS por sus siglas en inglés) ha sido usada exitosamente en el tratamiento de pacientes con enfermedad de Párkinson. La DBS tiene un electrodo que regula la actividad oscilatoria de los ganglios basales involucrados, como el núcleo subtalámico (STN). Un aspecto crítico en el implante de dicho electrodo es la localización precisa de la diana quirúrgica. Esta se realiza mediante imágenes pre-quirúrgicas, marcos estereotácticos y registros de micro-electrodos (MER). Este último permite visualizar la actividad eléctrica de diferentes estructuras a través del recorrido quirúrgico, cada una de ellas con un patrón de variaciones bien definidas en frecuencia; sin embargo, esto dista de ser un método automático o semi-automático que ayude al neurofisiólogo a tomar decisiones en cuanto a la diana quirúrgica. Con el ánimo de contribuir a la automatización, analizamos tres bandas de frecuencias de señales MER adquiridas en 11 pacientes sometidos a DBS: beta (13-40 Hz), gamma (40-200 Hz) y oscilaciones de alta frecuencia (HFO – 201-400 Hz). Se propusieron y evaluaron 5 índices para detectar el STN: variaciones de parámetros auto-regresivos y su derivada a lo largo del recorrido quirúrgico, la energía de cada banda a partir de la densidad espectral de potencia mediante el método de Yule-Walker, la relación de frecuencias altas a bajas y su derivada. Encontramos que la derivada de un parámetro de la banda beta y la relación alta-bajas de las bandas HFO/gamma alcanzaron errores en la localización del STN, similares a los reportados en la literatura (<2mm). Aunque los índices propuestos son sencillos de calcular y de fácil implementación en tiempo real, se deben seguir explorando para incrementar la capacidad de generalización de los resultados obtenidos

A functional micro-electrode mapping of ventral thalamus in Essential Tremor

Deep brain stimulation enables the delivery of therapeutic interventions to otherwise inaccessible areas of the brain while, at the same time, offering the unique opportunity to record from these same regions in awake patients. The posterior ventrolateral thalamus has become a reliable deep brain stimulation target for medically-refractory patients suffering from essential tremor. However, the contribution of the thalamus in essential tremor, and even whether posterior ventrolateral thalamus is the optimal target, remains a matter of ongoing debate. There are several lines of evidence supporting clusters of activity within the posterior ventrolateral thalamus that are important for tremor emergence. In this study we sought to map the functional properties of these clusters through microelectrode recordings during deep brain stimulation surgery. Data were obtained from 10 severely affected patients with essential tremor (12 hemispheres) undergoing deep brain stimulation surgery. Our results demonstrate power and coherence maxima located in the inferior posterior ventrolateral thalamus and immediate ventral region. Moreover, we identified distinct yet overlapping clusters of predominantly efferent (driving) and afferent (feedback) activity, with a preference for more efferent contributors, consistent with a net role in the driving of tremor output. Finally, we demonstrate that resolvable thalamic spiking activity directly relates to background activity and that the strength of tremor may be dictated by phase relationships between efferent and afferent pockets in the posterior ventrolateral thalamus. Taken together, these results provide important evidence for the role of the inferior posterior ventrolateral thalamus and its border region in essential tremor pathophysiology. Such results progress our mechanistic understanding and promote the adoption of next-generation therapies such as high resolution segregated deep brain stimulation electrodes

ELECTROPHYSIOLOGY OF BASAL GANGLIA (BG) CIRCUITRY AND DYSTONIA AS A MODEL OF MOTOR CONTROL DYSFUNCTION

The basal ganglia (BG) is a complex set of heavily interconnected nuclei located in the central part of the brain that receives inputs from the several areas of the cortex and projects via the thalamus back to the prefrontal and motor cortical areas. Despite playing a significant part in multiple brain functions, the physiology of the BG and associated disorders like dystonia remain poorly understood. Dystonia is a devastating condition characterized by ineffective, twisting movements, prolonged co-contractions and contorted postures. Evidences suggest that it occurs due to abnormal discharge patterning in BG-thalamocortocal (BGTC) circuitry. The central purpose of this study was to understand the electrophysiology of BGTC circuitry and its role in motor control and dystonia. Toward this goal, an advanced multi-target multi-unit recording and analysis system was utilized, which allows simultaneous collection and analysis of multiple neuronal units from multiple brain nuclei. Over the cause of this work, neuronal data from the globus pallidus (GP), subthalamic nucleus (STN), entopenduncular nucleus (EP), pallidal receiving thalamus (VL) and motor cortex (MC) was collected from normal, lesioned and dystonic rats under awake, head restrained conditions. The results have shown that the neuronal population in BG nuclei (GP, STN and EP) were characterized by a dichotomy of firing patterns in normal rats which remains preserved in dystonic rats. Unlike normals, neurons in dystonic rat exhibit reduced mean firing rate, increased irregularity and burstiness at resting state. The chaotic changes that occurs in BG leads to inadequate hyperpolarization levels within the VL thalamic neurons resulting in a shift from the normal bursting mode to an abnormal tonic firing pattern. During movement, the dystonic EP generates abnormally synchronized and elongated burst duration which further corrupts the VL motor signals. It was finally concluded that the loss of specificity and temporal misalignment between motor neurons leads to corrupted signaling to the muscles resulting in dystonic behavior. Furthermore, this study reveals the importance of EP output in controlling firing modes occurring in the VL thalamus

Effects of intracranial stimulation and the involvement of the human parahippocampal cortex in perception

How the human brain translates photons hitting the retina into conscious perception remains an open question. Throughout the medial temporal lobe (MTL), there are neurons (called concept cells) that change their firing rate when that neuron's preferred concept, e.g., a specific person or object, is seen. The firing rate of concept cells is correlated with perception. Nevertheless, it remains unclear whether or to what extent concept cells are involved in perceptogenesis, i.e., the creation of conscious percepts. Inferring from studies in monkeys, concept-specific neurons involved in perceptogenesis would be expected along the ventral and dorsal stream of visual processing (also called the what and where pathway, respectively). Various regions that are part of the dorsal stream are connected to the parahippocampal cortex (PHC), a region within the MTL. Compared to other MTL regions, lower selectivity, the absence of multimodal responses, and especially the shorter response latencies do not exclude an involvement of the PHC in perceptogenesis. In fact, damage to the parahippocampal place area (PPA, a part of the PHC) results in topographical disorientation. The goal of this thesis is to test the involvement of the PHC in perception by using electrical stimulation during a forced-choice categorization task involving landscapes versus animals. First, we determined effective parameters for intracranial stimulation of brain tissue in epilepsy patients implanted with depth-electrodes for seizure monitoring. We investigated the effects of amplitude, phase width, frequency, and pulse-train duration on neuronal firing, the local field potential (LFP), and behavioral responses to evoked percepts. Frequency and charge per phase were the most influential parameters on all three signals. Both parameters showed a positive effect on event-related potentials (ERPs) in the LFP. Higher frequencies (especially around 200 Hz) lead to a short-term inhibition of neuronal firing, while higher charge per phase can have an inhibitory or excitatory effect on neuronal firing. All parameters had a positive effect on the reports of evoked percepts; on reports of phosphenes in response to stimulating close to the optic radiation as well as on reports of auditory verbal hallucinations in response to stimulating Heschl's gyrus. Using functional magnetic resonance imaging (fMRI), we found that the PPA, i.e., the part of the PHC that is most selective towards images of landscapes, is rather small (up to 1‰ of total brain volume per hemisphere) with varying degrees of hemispheric laterality. Stimulating the PHC outside of the PPA - using a 100 ms high-frequency pulse train delivered at the natural response latency of the PHC - had no effect on categorizing landscapes. However, stimulating inside the PPA, close to the peak activation of the fMRI cluster, resulted in a 7% to 10% increase in landscape responses to ambiguous stimuli. Furthermore, stimulating the PPA also led to an increase in behavioral response time, especially to images with a predominant landscape component. None of our patients reported visual hallucinations of places or scenes in response to our stimulation protocols. Our data suggests that the PPA is involved in the perceptogenesis of landscapes at a stage that does not reach awareness, while the rest of the PHC is unlikely to be involved in perceptogenesis, at least not as it pertains to the perception of landscapes or animals. We also developed an online spike sorting algorithm and an adaptive screening procedure for concept cells to pave the way for new paradigms involving informed feedback

Computationally efficient algorithms and implementations of adaptive deep brain stimulation systems for Parkinson's disease

Clinical deep brain stimulation (DBS) is a tool used to mitigate pharmacologically intractable neurodegenerative diseases such as Parkinson's disease (PD), tremor and dystonia. Present implementations of DBS use continuous, high frequency voltage or current pulses so as to mitigate PD. This results in some limitations, among which there is stimulation induced side effects and shortening of pacemaker battery life. Adaptive DBS (aDBS) can be used to overcome a number of these limitations. Adaptive DBS is intended to deliver stimulation precisely only when needed. This thesis presents work undertaken to investigate, propose and develop novel algorithms and implementations of systems for adapting DBS. This thesis proposes four system implementations that could facilitate DBS adaptation either in the form of closed-loop DBS or spatial adaptation. The first method involved the use of dynamic detection to track changes in local field potentials (LFP) which can be indicative of PD symptoms. The work on dynamic detection included the synthesis of validation dataset using mainly autoregressive moving average (ARMA) models to enable the evaluation of a subset of PD detection algorithms for accuracy and complexity trade-offs. The subset of algorithms consisted of feature extraction (FE), dimensionality reduction (DR) and dynamic pattern classification stages. The combination with the best trade-off in terms of accuracy and complexity consisted of discrete wavelet transform (DWT) for FE, maximum ratio method (MRM) for DR and k-nearest neighbours (k-NN) for classification. The MRM is a novel DR method inspired by Fisher's separability criterion. The best combination achieved accuracy measures: F1-score of 97.9%, choice probability of 99.86% and classification accuracy of 99.29%. Regarding complexity, it had an estimated microchip area of 0.84 mm² for estimates in 90 nm CMOS process. The second implementation developed the first known PD detection and monitoring processor. This was achieved using complementary detection, which presents a hardware-efficient method of implementing a PD detection processor for monitoring PD progression in Parkinsonian patients. Complementary detection is achieved by using a combination of weak classifiers to produce a classifier with a higher consistency and confidence level than the individual classifiers in the configuration. The PD detection processor using the same processing stages as the first implementation was validated on an FPGA platform. By mapping the implemented design on a 45 nm CMOS process, the most optimal implementation achieved a dynamic power per channel of 2.26 μW and an area per channel of 0.2384 mm². It also achieved mean accuracy measures: Mathews correlation coefficient (MCC) of 0.6162, an F1-score of 91.38%, and mean classification accuracy of 91.91%. The third implementation proposed a framework for adapting DBS based on a critic-actor control approach. This models the relationship between a trained clinician (critic) and a neuro-modulation system (actor) for modulating DBS. The critic was implemented and validated using machine learning models, and the actor was implemented using a fuzzy controller. Therapy is modulated based on state estimates obtained through the machine learning models. PD suppression was achieved in seven out of nine test cases. The final implementation introduces spatial adaptation for aDBS. Spatial adaptation adjusts to variation in lead position and/or stimulation focus, as poor stimulation focus has been reported to affect therapeutic benefits of DBS. The implementation proposes dynamic current steering systems as a power-efficient implementation for multi-polar multisite current steering, with a particular focus on the output stage of the dynamic current steering system. The output stage uses dynamic current sources in implementing push-pull current sources that are interfaced to 16 electrodes so as to enable current steering. The performance of the output stage was demonstrated using a supply of 3.3 V to drive biphasic current pulses of up to 0.5 mA through its electrodes. The preliminary design of the circuit was implemented in 0.18 μm CMOS technology

Guiding deep brain stimulation neurosurgery with optical spectroscopy

Savoir différiencier les différentes types de tissus représente un aspect important lors d’interventions médicales, que ce soit pour aider au diagnostic d’une maladie ou pour le guidage chirurgical. Il est généralement très difficile de distinguer les tissus sains des tissus pathologiques à l’oeil nu et la navigation chirurgicale peut parfois être difficile dans les grands organes où la structure ciblé se trouve enfouie profondément. De nouvelles méthodes susceptibles d’accroître la réussite de telles interventions médicales suscitent actuellement de l’intérêt chez les professionnels de la santé. La spectroscopie optique, en analysant les interactions lumière-tissu dans une plage spectrale définie, est un outil permettant de différencier les tissus avec une résolution et une sensibilité bien supérieures à celles de l’oeil humain. Tout au long de cette thèse, je détaillerai comment la spectroscopie optique a été utilisée pour créer et améliorer un système de guidage optique utilisé pour la stimulation cérébrale profonde en neurochirurgie, en particulier pour le traitement de la maladie de Parkinson. Pour commencer, je montrerai comment les informations spectroscopiques peuvent fournir une rétroaction peropératoire en temps réel à un neurochirurgien, au cours de la phase d’implantation de la procédure, avec une sonde qui n’induit aucune invasion supplémentaire. Je présenterai l’investigation de deux modalités spectroscopiques différentes pour la discrimination tissulaire pour le guidage, soit la spectroscopie à réflectance diffuse et la spectroscopie de diffusion Raman anti-Stokes cohérente. Les avantages et les inconvénients des deux techniques, ainsi que leurs aptitude à la traduction prometteuse pour cette application seront abordés. Par la suite, je présenterai une nouvelle technique d’analyse de données pour extraire l’oxygénation des tissus à partir de spectres de réflectance diffus dans le but d’améliorer la précision de mesure en spectroscopie rétinienne et ultimement de porter un diagnostique. Bien que conçu pour la rétine, l’algorithme peut également être utilisé pour analyser les spectres acquis lors d’une neurochirurgie afin de fournir des informations à la fois discriminantes et diagnostiques. Finalement, je montrerai des preuves de diffusion anisotrope de la lumière dans les axones myélinisés de la moelle épinière et discuterai des conséquences que cela pourrait avoir sur les simulations actuelles de la propagation des photons dans le cerveau, qui feront partie intégrante d’un guidage optique efficace.Differentiating tissue types is an important aspect of guiding medical interventions whether it be for disease diagnosis or for surgical guidance. However, diseased and healthy tissues are often hard to discriminate by human vision alone and surgical navigation can be difficult to accomplish in large organs where the target structure lies deep within the body. New methods that can increase certainty in such medical interventions are therefore of great interest to healthcare professionals. Optical spectroscopy is a tool which can be exploited to probe discriminatory information in tissue by analyzing light-tissue interactions with a spectral range, resolution and sensitivity much greater than the human eye. Throughout this thesis, I will explain how I have leveraged optical spectroscopy to create, and improve, an optical guidance system for deep brain stimulation neurosurgery, specifically for the treatment of Parkinson’s disease. I will begin by describing how spectroscopic information can provide real-time feedback to a surgeon during the procedure, in the hopes of ultimately improving treatment outcome. To this end, I will present the investigation of two different spectroscopic modalities for optical guidance: diffuse reflectance spectroscopy, and coherent anti-Stokes Raman scattering spectroscopy. The advantages and disadvantages of both techniques will be discussed along with their promising translatability for this application. Following this, I will present a novel data analysis technique for extracting the tissue oxygenation from diffuse reflectance spectra with the aim of improved diagnostic information in retinal spectroscopy. While designed for the retina, the algorithm can also be used to analyze spectra acquired during a neurosurgery to provide both discriminatory and diagnostic information. Lastly, I will show evidence of anisotropic light scattering in the myelinated axons of the spinal cord and discuss the implications this may have on current photon propagation simulations in the brain, which will be integral for effective optical guidance