PyDBS: an automated image processing workflow for deep brain stimulation surgery

A technology framework for distributed preoperative planning and medical training in deep brain stimulation

Deep brain stimulation (DBS) is a groundbreaking therapy for movement disorders, necessitating precise planning and extensive training to ensure accurate electrode placement in critical brain regions, such as the thalamic nuclei. This paper introduces an innovative technology framework for DBS to support distributed, real-time preoperative planning and medical training. The system integrates advanced imaging techniques, interactive graphical representation, and real-time data synchronization to assist clinicians in accurately identifying essential anatomical structures and refining pre-surgical plans. At the platform's core are multi-volume rendering, segmentation, and virtual tool modeling algorithms that employ transparency and refinement controls to seamlessly merge and visualize different tissue types in 3D alongside their interactions with surgical tools. This method enhances visual clarity and provides a highly detailed depiction of crucial structures, ensuring the precision required for effective DBS planning. By delivering dynamic, real-time feedback, the framework supports improved decision-making and sets a new standard for collaborative DBS training and procedural preparation. The platform's web-based synchronization architecture enhances collaboration by allowing neurologists and surgeons to simultaneously interact with visualized data from any location. This functionality supports live feedback, promotes collaborative decision-making, and streamlines procedural planning, leading to improved surgical outcomes. Performance evaluations across various hardware configurations and web browsers demonstrate the platform's high rendering speed and low-latency data synchronization, ensuring responsive and reliable interactions essential for clinical use. Its adaptability makes it suitable for medical training, preoperative planning, and intraoperative support, accommodating a wide range of hardware setups and web environments to address the specific demands of DBS-related procedures. This research lays a robust foundation for advancing distributed clinical planning, comprehensive medical education, and improved patient care in neurostimulation therapies.

aXonica: A support package for MRI based Neuroimaging

Magnetic Resonance Imaging (MRI) assists in studying the nervous system. MRI scans undergo significant processing before presenting the final images to medical practitioners. These processes are executed with ease due to excellent software pipelines. However, establishing software workstations is non-trivial and requires researchers in life sciences to be comfortable in downloading, installing, and scripting software that is non-user-friendly and may lack basic GUI. As researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines speeding up building software workstations and laboratories. Previous solutions include NeuroDebian, BIDS Apps, Flywheel, QMENTA, Boutiques, Brainlife and Neurodesk. Overall, all these solutions complement each other. NeuroDebian covers neuroscience and has a wider scope, providing only 51 tools for MRI. Whereas, BIDS Apps is committed to the BIDS format, covering only 45 software related to MRI. Boutiques is more flexible, facilitating its pipelines to be easily installed as separate containers, validated, published, and executed. Whereas, both Flywheel and Qmenta are propriety, leaving four for users looking for 'free for use' tools, i.e., NeuroDebian, Brainlife, Neurodesk, and BIDS Apps. This paper presents an extensive survey of 317 tools published in MRI-based neuroimaging in the last ten years, along with 'aXonica,' an MRI-based neuroimaging support package that is unbiased towards any formatting standards and provides 130 applications, more than that of NeuroDebian (51), BIDS App (45), Flywheel (70), and Neurodesk (85). Using a technology stack that employs GUI as the front-end and shell scripted back-end, aXonica provides (i) 130 tools that span the entire MRI-based neuroimaging analysis, and allow the user to (ii) select the software of their choice, (iii) automatically resolve individual dependencies and (iv) installs them. Hence, aXonica can serve as an important resource for researchers and teachers working in the field of MRI-based Neuroimaging to (a) develop software workstations, and/or (b) install newer tools in their existing workstations.

Improved segmentation of basal ganglia from MR images using convolutional neural network with crossover-typed skip connection

PURPOSE

Accurate and automatic segmentation of basal ganglia from magnetic resonance (MR) images is important for diagnosis and treatment of various brain disorders. However, the basal ganglia segmentation is a challenging task because of the class imbalance and the unclear boundaries among basal ganglia anatomical structures. Thus, we aim to present an encoder-decoder convolutional neural network (CNN)-based method for improved segmentation of basal ganglia by focusing on skip connections that determine the segmentation performance of encoder-decoder CNNs. We also aim to reveal the effect of skip connections on the segmentation of basal ganglia with unclear boundaries.

METHODS

We used the encoder-decoder CNNs with the following five patterns of skip connections: without skip connection, with full-resolution horizontal skip connection, with horizontal skip connections, with vertical skip connections, and with crossover-typed skip connections (the proposed method). We compared and evaluated the performance of the CNNs in the experiment of basal ganglia segmentation using T1-weighted MR brain images of 79 patients.

RESULTS

The experimental results showed that the skip connections at each scale level help CNNs to acquire multi-scale image features, the vertical skip connections contribute on acquiring finer image features for segmentation of smaller anatomical structures with more blurred boundaries, and the crossover-typed skip connections, a combination of horizontal and vertical skip connections, provided better segmentation accuracy.

CONCLUSION

This paper investigated the effect of skip connections on the basal ganglia segmentation and revealed the crossover-typed skip connections might be effective for improving the segmentation of basal ganglia with the class imbalance and the unclear boundaries.

Combining simple interactivity and machine learning: a separable deep learning approach to subthalamic nucleus localization and segmentation in MRI for deep brain stimulation surgical planning

Purpose: Deep brain stimulation (DBS) is an interventional treatment for some neurological and neurodegenerative diseases. For example, in Parkinson's disease, DBS electrodes are positioned at particular locations within the basal ganglia to alleviate the patient's motor symptoms. These interventions depend greatly on a preoperative planning stage in which potential targets and electrode trajectories are identified in a preoperative MRI. Due to the small size and low contrast of targets such as the subthalamic nucleus (STN), their segmentation is a difficult task. Machine learning provides a potential avenue for development, but it has difficulty in segmenting such small structures in volumetric images due to additional problems such as segmentation class imbalance. Approach: We present a two-stage separable learning workflow for STN segmentation consisting of a localization step that detects the STN and crops the image to a small region and a segmentation step that delineates the structure within that region. The goal of this decoupling is to improve accuracy and efficiency and to provide an intermediate representation that can be easily corrected by a clinical user. This correction capability was then studied through a human-computer interaction experiment with seven novice participants and one expert neurosurgeon. Results: Our two-step segmentation significantly outperforms the comparative registration-based method currently used in clinic and approaches the fundamental limit on variability due to the image resolution. In addition, the human-computer interaction experiment shows that the additional interaction mechanism allowed by separating STN segmentation into two steps significantly improves the users' ability to correct errors and further improves performance. Conclusions: Our method shows that separable learning not only is feasible for fully automatic STN segmentation but also leads to improved interactivity that can ease its translation into clinical use.

Somatotopic Organization of Hyperdirect Pathway Projections From the Primary Motor Cortex in the Human Brain

Background

The subthalamic nucleus (STN) is an effective neurosurgical target to improve motor symptoms in Parkinson's Disease (PD) patients. MR-guided Focused Ultrasound (MRgFUS) subthalamotomy is being explored as a therapeutic alternative to Deep Brain Stimulation (DBS) of the STN. The hyperdirect pathway provides a direct connection between the cortex and the STN and is likely to play a key role in the therapeutic effects of MRgFUS intervention in PD patients.

Objective

This study aims to investigate the topography and somatotopy of hyperdirect pathway projections from the primary motor cortex (M1).

Methods

We used advanced multi-fiber tractography and high-resolution diffusion MRI data acquired on five subjects of the Human Connectome Project (HCP) to reconstruct hyperdirect pathway projections from M1. Two neuroanatomy experts reviewed the anatomical accuracy of the tracts. We extracted the fascicles arising from the trunk, arm, hand, face and tongue area from the reconstructed pathways. We assessed the variability among subjects based on the fractional anisotropy (FA) and mean diffusivity (MD) of the fibers. We evaluated the spatial arrangement of the different fascicles using the Dice Similarity Coefficient (DSC) of spatial overlap and the centroids of the bundles.

Results

We successfully reconstructed hyperdirect pathway projections from M1 in all five subjects. The tracts were in agreement with the expected anatomy. We identified hyperdirect pathway fascicles projecting from the trunk, arm, hand, face and tongue area in all subjects. Tract-derived measurements showed low variability among subjects, and similar distributions of FA and MD values among the fascicles projecting from different M1 areas. We found an anterolateral somatotopic arrangement of the fascicles in the corona radiata, and an average overlap of 0.63 in the internal capsule and 0.65 in the zona incerta.

Conclusion

Multi-fiber tractography combined with high-resolution diffusion MRI data enables the identification of the somatotopic organization of the hyperdirect pathway. Our preliminary results suggest that the subdivisions of the hyperdirect pathway projecting from the trunk, arm, hand, face, and tongue motor area are intermixed at the level of the zona incerta and posterior limb of the internal capsule, with a predominantly overlapping topographical organization in both regions. Subject-specific knowledge of the hyperdirect pathway somatotopy could help optimize target definition in MRgFUS intervention.

Deciphering the Network Effects of Deep Brain Stimulation in Parkinson's Disease

INTRODUCTION

Deep brain stimulation of the subthalamic nucleus (STN-DBS) is an established therapy for Parkinson's disease (PD). However, a more detailed characterization of the targeted network and its grey matter (GM) terminals that drive the clinical outcome is needed. In this direction, the use of MRI after DBS surgery is now possible due to recent advances in hardware, opening a window for the clarification of the association between the affected tissue, including white matter fiber pathways and modulated GM regions, and the DBS-related clinical outcome. Therefore, we present a computational framework for reconstruction of targeted networks on postoperative MRI.

METHODS

We used a combination of preoperative whole-brain T1-weighted (T1w) and diffusion-weighted MRI data for morphometric integrity assessment and postoperative T1w MRI for electrode reconstruction and network reconstruction in 15 idiopathic PD patients. Within this framework, we made use of DBS lead artifact intensity profiles on postoperative MRI to determine DBS locations used as seeds for probabilistic tractography to cortical and subcortical targets within the motor circuitry. Lastly, we evaluated the relationship between brain microstructural characteristics of DBS-targeted brain network terminals and postoperative clinical outcomes.

RESULTS

The proposed framework showed robust performance for identifying the DBS electrode positions. Connectivity profiles between the primary motor cortex (M1), supplementary motor area (SMA), and DBS locations were strongly associated with the stimulation intensity needed for the optimal clinical outcome. Local diffusion properties of the modulated pathways were related to DBS outcomes. STN-DBS motor symptom improvement was highly associated with cortical thickness in the middle frontal and superior frontal cortices, but not with subcortical volumetry.

CONCLUSION

These data suggest that STN-DBS outcomes largely rely on the modulatory interference from cortical areas, particularly M1 and SMA, to DBS locations.

Linking immune-mediated damage to neurodegeneration in multiple sclerosis: could network-based MRI help?

Inflammatory demyelination characterizes the initial stages of multiple sclerosis, while progressive axonal and neuronal loss are coexisting and significantly contribute to the long-term physical and cognitive impairment. There is an unmet need for a conceptual shift from a dualistic view of multiple sclerosis pathology, involving either inflammatory demyelination or neurodegeneration, to integrative dynamic models of brain reorganization, where, glia-neuron interactions, synaptic alterations and grey matter pathology are longitudinally envisaged at the whole-brain level. Functional and structural MRI can delineate network hallmarks for relapses, remissions or disease progression, which can be linked to the pathophysiology behind inflammatory attacks, repair and neurodegeneration. Here, we aim to unify recent findings of grey matter circuits dynamics in multiple sclerosis within the framework of molecular and pathophysiological hallmarks combined with disease-related network reorganization, while highlighting advances from animal models (in vivo and ex vivo) and human clinical data (imaging and histological). We propose that MRI-based brain networks characterization is essential for better delineating ongoing pathology and elaboration of particular mechanisms that may serve for accurate modelling and prediction of disease courses throughout disease stages.

Artificial Intelligence in Brain Tumour Surgery-An Emerging Paradigm

Artificial intelligence (AI) platforms have the potential to cause a paradigm shift in brain tumour surgery. Brain tumour surgery augmented with AI can result in safer and more effective treatment. In this review article, we explore the current and future role of AI in patients undergoing brain tumour surgery, including aiding diagnosis, optimising the surgical plan, providing support during the operation, and better predicting the prognosis. Finally, we discuss barriers to the successful clinical implementation, the ethical concerns, and we provide our perspective on how the field could be advanced.

Promises and Perils of Artificial Intelligence in Neurosurgery

Artificial intelligence (AI)-facilitated clinical automation is expected to become increasingly prevalent in the near future. AI techniques may permit rapid and detailed analysis of the large quantities of clinical data generated in modern healthcare settings, at a level that is otherwise impossible by humans. Subsequently, AI may enhance clinical practice by pushing the limits of diagnostics, clinical decision making, and prognostication. Moreover, if combined with surgical robotics and other surgical adjuncts such as image guidance, AI may find its way into the operating room and permit more accurate interventions, with fewer errors. Despite the considerable hype surrounding the impending medical AI revolution, little has been written about potential downsides to increasing clinical automation. These may include both direct and indirect consequences. Directly, faulty, inadequately trained, or poorly understood algorithms may produce erroneous results, which may have wide-scale impact. Indirectly, increasing use of automation may exacerbate de-skilling of human physicians due to over-reliance, poor understanding, overconfidence, and lack of necessary vigilance of an automated clinical workflow. Many of these negative phenomena have already been witnessed in other industries that have already undergone, or are undergoing "automation revolutions," namely commercial aviation and the automotive industry. This narrative review explores the potential benefits and consequences of the anticipated medical AI revolution from a neurosurgical perspective.

Surgical planning assistance in keyhole and percutaneous surgery: A systematic review

Surgical planning of percutaneous interventions has a crucial role to guarantee the success of minimally invasive surgeries. In the last decades, many methods have been proposed to reduce clinician work load related to the planning phase and to augment the information used in the definition of the optimal trajectory. In this survey, we include 113 articles related to computer assisted planning (CAP) methods and validations obtained from a systematic search on three databases. First, a general formulation of the problem is presented, independently from the surgical field involved, and the key steps involved in the development of a CAP solution are detailed. Secondly, we categorized the articles based on the main surgical applications, which have been object of study and we categorize them based on the type of assistance provided to the end-user.

Evaluation of Automatic Segmentation of Thalamic Nuclei through Clinical Effects Using Directional Deep Brain Stimulation Leads: A Technical Note

Automatic anatomical segmentation of patients’ anatomical structures and modeling of the volume of tissue activated (VTA) can potentially facilitate trajectory planning and post-operative programming in deep brain stimulation (DBS). We demonstrate an approach to evaluate the accuracy of such software for the ventral intermediate nucleus (VIM) using directional leads. In an essential tremor patient with asymmetrical brain anatomy, lead placement was adjusted according to the suggested segmentation made by the software (Brainlab). Postoperatively, we used directionality to assess lead placement using side effect testing (internal capsule and sensory thalamus). Clinical effects were then compared to the patient-specific visualization and VTA simulation in the GUIDE™ XT software (Boston Scientific). The patient’s asymmetrical anatomy was correctly recognized by the software and matched the clinical results. VTA models matched best for dysarthria (6 out of 6 cases) and sensory hand side effects (5/6), but least for facial side effects (1/6). Best concordance was observed for the modeled current anterior and back spread of the VTA, worst for the current side spread. Automatic anatomical segmentation and VTA models can be valuable tools for DBS planning and programming. Directional DBS leads allow detailed postoperative assessment of the concordance of such image-based simulation and visualization with clinical effects.

Image Guidance in Deep Brain Stimulation Surgery to Treat Parkinson's Disease: A Comprehensive Review

Deep brain stimulation (DBS) is an effective therapy as an alternative to pharmaceutical treatments for Parkinson's disease (PD). Aside from factors such as instrumentation, treatment plans, and surgical protocols, the success of the procedure depends heavily on the accurate placement of the electrode within the optimal therapeutic targets while avoiding vital structures that can cause surgical complications and adverse neurologic effects. Although specific surgical techniques for DBS can vary, interventional guidance with medical imaging has greatly contributed to the development, outcomes, and safety of the procedure. With rapid development in novel imaging techniques, computational methods, and surgical navigation software, as well as growing insights into the disease and mechanism of action of DBS, modern image guidance is expected to further enhance the capacity and efficacy of the procedure in treating PD. This article surveys the state-of-the-art techniques in image-guided DBS surgery to treat PD, and discusses their benefits and drawbacks, as well as future directions on the topic.

Stimulation maps: visualization of results of quantitative intraoperative testing for deep brain stimulation surgery

Deep brain stimulation (DBS) is an established therapy for movement disorders such as essential tremor (ET). Positioning of the DBS lead in the patient's brain is crucial for effective treatment. Extensive evaluations of improvement and adverse effects of stimulation at different positions for various current amplitudes are performed intraoperatively. However, to choose the optimal position of the lead, the information has to be "mentally" visualized and analyzed. This paper introduces a new technique called "stimulation maps," which summarizes and visualizes the high amount of relevant data with the aim to assist in identifying the optimal DBS lead position. It combines three methods: outlines of the relevant anatomical structures, quantitative symptom evaluation, and patient-specific electric field simulations. Through this combination, each voxel in the stimulation region is assigned one value of symptom improvement, resulting in the division of stimulation region into areas with different improvement levels. This technique was applied retrospectively to five ET patients in the University Hospital in Clermont-Ferrand, France. Apart from identifying the optimal implant position, the resultant nine maps show that the highest improvement region is frequently in the posterior subthalamic area. The results demonstrate the utility of the stimulation maps in identifying the optimal implant position. Graphical abstract.

Conscious and unconscious expectancy effects: A behavioral, scalp and intracranial electroencephalography study

OBJECTIVE

The scope of unconscious cognition stretched its limits dramatically during the last 40 years, yet most unconscious processes and representations that have been described so far are fleeting and very short-lived, whereas conscious representations can be actively maintained in working memory for a virtually unlimited period. In the present work we aimed at exploring conscious and unconscious lasting (>1 second) expectancy effects.

METHODS

In a series of four experiments we engaged participants in the foreperiod paradigm while using both unmasked and masked cues that were informative about the presence/absence of an upcoming target. We recorded behavioral responses, high-density scalp EEG (Exp. 2a), and intra-cranial EEG (Exp. 2b).

RESULTS

While conscious expectancy was associated with a large behavioral effect (~150 ms), unconscious expectancy effect was significant but much smaller (4 ms). Both conscious and unconscious expectancy Contingent Negative Variations (CNVs) originated from temporal cortices, but only the late component of conscious CNV originated from an additional source located in the vicinity of mesio-frontal areas and supplementary motor areas. Finally, only conscious expectancy was accessible to introspection.

CONCLUSIONS

Both unmasked and masked cues had an impact on response times and on brain activity.

SIGNIFICANCE

These results support a two-stage model of the underlying mechanisms of expectancy.

Multi-modal imaging with specialized sequences improves accuracy of the automated subcortical grey matter segmentation

The basal ganglia and limbic system, particularly the thalamus, putamen, internal and external globus pallidus, substantia nigra, and sub-thalamic nucleus, comprise a clinically relevant signal network for Parkinson's disease. In order to manually trace these structures, a combination of high-resolution and specialized sequences at 7 T are used, but it is not feasible to routinely scan clinical patients in those scanners. Targeted imaging sequences at 3 T have been presented to enhance contrast in a select group of these structures. In this work, we show that a series of atlases generated at 7 T can be used to accurately segment these structures at 3 T using a combination of standard and optimized imaging sequences, though no one approach provided the best result across all structures. In the thalamus and putamen, a median Dice Similarity Coefficient (DSC) over 0.88 and a mean surface distance <1.0 mm were achieved using a combination of T1 and an optimized inversion recovery imaging sequences. In the internal and external globus pallidus a DSC over 0.75 and a mean surface distance <1.2 mm were achieved using a combination of T1 and inversion recovery imaging sequences. In the substantia nigra and sub-thalamic nucleus a DSC of over 0.6 and a mean surface distance of <1.0 mm were achieved using the inversion recovery imaging sequence. On average, using T1 and optimized inversion recovery together significantly improved segmentation results than over individual modality (p < 0.05 Wilcoxon sign-rank test).

Automatic localization of the subthalamic nucleus on patient-specific clinical MRI by incorporating 7 T MRI and machine learning: Application in deep brain stimulation

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) has shown clinical potential for relieving the motor symptoms of advanced Parkinson's disease. While accurate localization of the STN is critical for consistent across-patients effective DBS, clear visualization of the STN under standard clinical MR protocols is still challenging. Therefore, intraoperative microelectrode recordings (MER) are incorporated to accurately localize the STN. However, MER require significant neurosurgical expertise and lengthen the surgery time. Recent advances in 7 T MR technology facilitate the ability to clearly visualize the STN. The vast majority of centers, however, still do not have 7 T MRI systems, and fewer have the ability to collect and analyze the data. This work introduces an automatic STN localization framework based on standard clinical MRIs without additional cost in the current DBS planning protocol. Our approach benefits from a large database of 7 T MRI and its clinical MRI pairs. We first model in the 7 T database, using efficient machine learning algorithms, the spatial and geometric dependency between the STN and its adjacent structures (predictors). Given a standard clinical MRI, our method automatically computes the predictors and uses the learned information to predict the patient-specific STN. We validate our proposed method on clinical T2 W MRI of 80 subjects, comparing with experts-segmented STNs from the corresponding 7 T MRI pairs. The experimental results show that our framework provides more accurate and robust patient-specific STN localization than using state-of-the-art atlases. We also demonstrate the clinical feasibility of the proposed technique assessing the post-operative electrode active contact locations.

Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging

Deep brain stimulation (DBS) is a highly efficacious treatment option for movement disorders and a growing number of other indications are investigated in clinical trials. To ensure optimal treatment outcome, exact electrode placement is required. Moreover, to analyze the relationship between electrode location and clinical results, a precise reconstruction of electrode placement is required, posing specific challenges to the field of neuroimaging. Since 2014 the open source toolbox Lead-DBS is available, which aims at facilitating this process. The tool has since become a popular platform for DBS imaging. With support of a broad community of researchers worldwide, methods have been continuously updated and complemented by new tools for tasks such as multispectral nonlinear registration, structural/functional connectivity analyses, brain shift correction, reconstruction of microelectrode recordings and orientation detection of segmented DBS leads. The rapid development and emergence of these methods in DBS data analysis require us to revisit and revise the pipelines introduced in the original methods publication. Here we demonstrate the updated DBS and connectome pipelines of Lead-DBS using a single patient example with state-of-the-art high-field imaging as well as a retrospective cohort of patients scanned in a typical clinical setting at 1.5T. Imaging data of the 3T example patient is co-registered using five algorithms and nonlinearly warped into template space using ten approaches for comparative purposes. After reconstruction of DBS electrodes (which is possible using three methods and a specific refinement tool), the volume of tissue activated is calculated for two DBS settings using four distinct models and various parameters. Finally, four whole-brain tractography algorithms are applied to the patient's preoperative diffusion MRI data and structural as well as functional connectivity between the stimulation volume and other brain areas are estimated using a total of eight approaches and datasets. In addition, we demonstrate impact of selected preprocessing strategies on the retrospective sample of 51 PD patients. We compare the amount of variance in clinical improvement that can be explained by the computer model depending on the preprocessing method of choice. This work represents a multi-institutional collaborative effort to develop a comprehensive, open source pipeline for DBS imaging and connectomics, which has already empowered several studies, and may facilitate a variety of future studies in the field.

Comparison of interactive and automatic segmentation of stereoelectroencephalography electrodes on computed tomography post-operative images: preliminary results

Stereoelectroencephalography is a surgical procedure used in the treatment of pharmacoresistant epilepsy. Multiple electrodes are inserted in the patient's brain in order to record the electrical activity and detect the epileptogenic zone at the source of the seizures. An accurate localisation of their contacts on post-operative images is a crucial step to interpret the recorded signals and achieve a successful resection afterwards. In this Letter, the authors propose interactive and automatic methods to help the surgeon with the segmentation of the electrodes and their contacts. Then, they present a preliminary comparison of the methods in terms of accuracy and processing time through experimental measurements performed by two users, and discuss these first results. The final purpose of this work is to assist the neurosurgeons and neurologists in the contacts localisation procedure, make it faster, more precise and less tedious.

ESM-CT: a precise method for localization of DBS electrodes in CT images

BACKGROUND

Deep brain stimulation (DBS) of the subthalamic nucleus produces variable effects in Parkinson disease. Variation may result from different electrode positions relative to target. Thus, precise electrode localization is crucial when investigating DBS effects.

NEW METHOD

We developed a semi-automated method, Electrode Shaft Modeling in CT images (ESM-CT) to reconstruct DBS lead trajectories and contact locations. We evaluated methodological sensitivity to operator-dependent steps, robustness to image resampling, and test-retest replicability. ESM-CT was applied in 56 patients to study electrode position change (and relation to time between scans, postoperative subdural air volume, and head tilt during acquisition) between images acquired immediately post-implantation (DBS-CT) and months later (DEL-CT).

RESULTS

Electrode tip localization was robust to image resampling and replicable to within ∼ 0.2 mm on test-retest comparisons. Systematic electrode displacement occurred rostral-ventral-lateral between DBS-CT and DEL-CT scans. Head angle was a major explanatory factor (p < 0.001,Pearson's r = 0.46, both sides) and volume of subdural air weakly predicted electrode displacement (p = 0.02,r = 0.29:p = 0.1,r = 0.25 for left:right). Modeled shaft curvature was slightly greater in DEL-CT. Magnitude of displacement and degree of curvature were independent of elapsed time between scans.

COMPARISON WITH EXISTING METHODS

Comparison of ESM-CT against two existing methods revealed systematic differences in one coordinate (1 ± 0.3 mm,p < 0.001) for one method and in three coordinates for another method (x:0.1 ± 0.1 mm, y:0.4 ± 0.2 mm, z:0.4 ± 0.2 mm, p < 10-10). Within-method coordinate variability across participants is similar.

CONCLUSION

We describe a robust and precise method for CT DBS contact localization. Application revealed that acquisition head angle significantly impacts electrode position. DBS localization schemes should account for head angle.

Functional atlases for analysis of motor and neuropsychological outcomes after medial globus pallidus and subthalamic stimulation

Anatomical atlases have been developed to improve the targeting of basal ganglia in deep brain stimulation. However, the sole anatomy cannot predict the functional outcome of this surgery. Deep brain stimulation is often a compromise between several functional outcomes: motor, fluency and neuropsychological outcomes in particular. In this study, we have developed anatomo-clinical atlases for the targeting of subthalamic and medial globus pallidus deep brain stimulation. The activated electrode coordinates of 42 patients implanted in the subthalamic nucleus and 29 patients in the medial globus pallidus were studied. The atlas was built using the representation of the volume of tissue theoretically activated by the stimulation. The UPDRS score was used to represent the motor outcome. The Stroop test was represented as well as semantic and phonemic fluencies. For the subthalamic nucleus, best motor outcomes were obtained when the supero-lateral part of the nucleus was stimulated whereas the semantic fluency was impaired in this same region. For the medial globus pallidus, best outcomes were obtained when the postero ventral part of the nucleus was stimulated whereas the phonemic fluency was impaired in this same region. There was no significant neuropsychological impairment. We have proposed new anatomo-clinical atlases to visualize the motor and neuropsychological consequences at 6 months of subthalamic nucleus and pallidal stimulation in patients with Parkinson's disease.

Automatic segmentation of stereoelectroencephalography (SEEG) electrodes post-implantation considering bending

Purpose

The accurate and automatic localisation of SEEG electrodes is crucial for determining the location of epileptic seizure onset. We propose an algorithm for the automatic segmentation of electrode bolts and contacts that accounts for electrode bending in relation to regional brain anatomy.

Methods

Co-registered post-implantation CT, pre-implantation MRI, and brain parcellation images are used to create regions of interest to automatically segment bolts and contacts. Contact search strategy is based on the direction of the bolt with distance and angle constraints, in addition to post-processing steps that assign remaining contacts and predict contact position. We measured the accuracy of contact position, bolt angle, and anatomical region at the tip of the electrode in 23 post-SEEG cases comprising two different surgical approaches when placing a guiding stylet close to and far from target point. Local and global bending are computed when modelling electrodes as elastic rods.

Results

Our approach executed on average in 36.17 s with a sensitivity of 98.81% and a positive predictive value (PPV) of 95.01%. Compared to manual segmentation, the position of contacts had a mean absolute error of 0.38 mm and the mean bolt angle difference of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.59^{\circ }$$\end{document}0.59∘ resulted in a mean displacement error of 0.68 mm at the tip of the electrode. Anatomical regions at the tip of the electrode were in strong concordance with those selected manually by neurosurgeons, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ICC(3,k)=0.76$$\end{document}ICC(3,k)=0.76, with average distance between regions of 0.82 mm when in disagreement. Our approach performed equally in two surgical approaches regardless of the amount of electrode bending.

Conclusion

We present a method robust to electrode bending that can accurately segment contact positions and bolt orientation. The techniques presented in this paper will allow further characterisation of bending within different brain regions.

Electronic supplementary material

The online version of this article (10.1007/s11548-018-1740-8) contains supplementary material, which is available to authorized users.

Automatic preoperative planning of DBS electrode placement using anatomo-clinical atlases and volume of tissue activated

PURPOSE

Deep brain stimulation (DBS) is a procedure requiring accurate targeting and electrode placement. The two key elements for successful planning are preserving patient safety by ensuring a safe trajectory and creating treatment efficacy through optimal selection of the stimulation point. In this work, we present the first approach of computer-assisted preoperative DBS planning to automatically optimize both the safety of the electrode's trajectory and location of the stimulation point so as to provide the best clinical outcome.

METHODS

Building upon the findings of previous works focused on electrode trajectory, we added a set of constraints guiding the choice of stimulation point. These took into account retrospective data represented by anatomo-clinical atlases and intersections between the stimulation region and sensitive anatomical structures causing side effects. We implemented our method into automatic preoperative planning software to assess if the algorithm was able to simultaneously optimize electrode trajectory and the stimulation point.

RESULTS

Leave-one-out cross-validation on a dataset of 18 cases demonstrated an improvement in the expected outcome when using the new constraints. The distance to critical structures was not reduced. The intersection between the stimulation region and structures sensitive to stimulation was minimized.

CONCLUSIONS

Introducing these new constraints guided the planning to select locations showing a trend toward symptom improvement, while minimizing the risks of side effects, and there was no cost in terms of trajectory safety.

DBStar: An Open-Source Tool Kit for Imaging Analysis with Patient-Customized Deep Brain Stimulation Platforms

BACKGROUND/OBJECTIVES

To create an open-source method for reconstructing microelectrode recording (MER) and deep brain stimulation (DBS) electrode coordinates along multiple parallel trajectories with patient-specific DBS implantation platforms to facilitate DBS research.

METHODS

We combined the surgical geometry (extracted from WayPoint Planner), pre-/intra-/postoperative computed tomography (CT) and/or magnetic resonance (MR) images, and integrated them into the Analysis of Functional NeuroImages (AFNI) neuroimaging analysis environment using functions written in Python. Electrode coordinates were calculated from image-based electrode surfaces and recording trajectory depth values. Coordinates were translated into appropriate trajectories, and were tested for proximity to patient-specific or atlas-based anatomical structures. Final DBS electrode coordinates for 3 patient populations (ventral intermediate nucleus [VIM], subthalamic nucleus [STN], and globus pallidus pars interna [GPi]) were calculated. For STN cases, MER site coordinates were then analyzed to see whether they were inside or outside the STN.

RESULTS

Final DBS electrode coordinates were described for VIM, STN, and GPi patient populations. 115/169 (68%) STN MER sites were within 1 mm of the STN in AFNI's Talairach and Tournoux (TT) atlas.

CONCLUSIONS

DBStar is a robust tool kit for understanding the anatomical location and context of electrode locations, and can easily be used for imaging, behavioral, or electrophysiological analyses.

PaCER - A fully automated method for electrode trajectory and contact reconstruction in deep brain stimulation

Deep brain stimulation (DBS) is a neurosurgical intervention where electrodes are permanently implanted into the brain in order to modulate pathologic neural activity. The post-operative reconstruction of the DBS electrodes is important for an efficient stimulation parameter tuning. A major limitation of existing approaches for electrode reconstruction from post-operative imaging that prevents the clinical routine use is that they are manual or semi-automatic, and thus both time-consuming and subjective. Moreover, the existing methods rely on a simplified model of a straight line electrode trajectory, rather than the more realistic curved trajectory. The main contribution of this paper is that for the first time we present a highly accurate and fully automated method for electrode reconstruction that considers curved trajectories. The robustness of our proposed method is demonstrated using a multi-center clinical dataset consisting of N = 44 electrodes. In all cases the electrode trajectories were successfully identified and reconstructed. In addition, the accuracy is demonstrated quantitatively using a high-accuracy phantom with known ground truth. In the phantom experiment, the method could detect individual electrode contacts with high accuracy and the trajectory reconstruction reached an error level below 100 μm (0.046 ± 0.025 mm). An implementation of the method is made publicly available such that it can directly be used by researchers or clinicians. This constitutes an important step towards future integration of lead reconstruction into standard clinical care.

Vocal emotion decoding in the subthalamic nucleus: An intracranial ERP study in Parkinson's disease

Using intracranial local field potential (LFP) recordings in patients with Parkinson's disease (PD) undergoing deep brain stimulation (DBS), we explored the electrophysiological activity of the subthalamic nucleus (STN) in response to emotional stimuli in the auditory modality. Previous studies focused on the influence of visual stimuli. To this end, we recorded LFPs within the STN in response to angry, happy, and neutral prosodies in 13 patients with PD who had just undergone implantation of DBS electrodes. We observed specific modulation of the right STN in response to anger and happiness, as opposed to neutral prosody, occurring at around 200-300ms post-onset, and later at around 850-950ms post-onset for anger and at around 3250-3350ms post-onset for happiness. Taken together with previous reports of modulated STN activity in response to emotional visual stimuli, the present results appear to confirm that the STN is involved in emotion processing irrespective of stimulus valence and sensory modality.

In vivo Exploration of the Connectivity between the Subthalamic Nucleus and the Globus Pallidus in the Human Brain Using Multi-Fiber Tractography

The basal ganglia is part of a complex system of neuronal circuits that play a key role in the integration and execution of motor, cognitive and emotional function in the human brain. Parkinson’s disease is a progressive neurological disorder of the motor circuit characterized by tremor, rigidity, and slowness of movement. Deep brain stimulation (DBS) of the subthalamic nucleus and the globus pallidus pars interna provides an efficient treatment to reduce symptoms and levodopa-induced side effects in Parkinson’s disease patients. While the underlying mechanism of action of DBS is still unknown, the potential modulation of white matter tracts connecting the surgical targets has become an active area of research. With the introduction of advanced diffusion MRI acquisition sequences and sophisticated post-processing techniques, the architecture of the human brain white matter can be explored in vivo. The goal of this study is to investigate the white matter connectivity between the subthalamic nucleus and the globus pallidus. Two multi-fiber tractography methods were used to reconstruct pallido-subthalamic, subthalamo-pallidal and pyramidal fibers in five healthy subjects datasets of the Human Connectome Project. The anatomical accuracy of the tracts was assessed by four judges with expertise in neuroanatomy, functional neurosurgery, and diffusion MRI. The variability among subjects was evaluated based on the fractional anisotropy and mean diffusivity of the tracts. Both multi-fiber approaches enabled the detection of complex fiber architecture in the basal ganglia. The qualitative evaluation by experts showed that the identified tracts were in agreement with the expected anatomy. Tract-derived measurements demonstrated relatively low variability among subjects. False-negative tracts demonstrated the current limitations of both methods for clinical decision-making. Multi-fiber tractography methods combined with state-of-the-art diffusion MRI data have the potential to help identify white matter tracts connecting DBS targets in functional neurosurgery intervention.

Improvement of Pyramidal Tract Side Effect Prediction Using a Data-Driven Method in Subthalamic Stimulation

OBJECTIVE

subthalamic nucleus deep brain stimulation (STN DBS) is limited by the occurrence of a pyramidal tract side effect (PTSE) induced by electrical activation of the pyramidal tract. Predictive models are needed to assist the surgeon during the electrode trajectory preplanning. The objective of the study was to compare two methods of PTSE prediction based on clinical assessment of PTSE induced by STN DBS in patients with Parkinson's disease.

METHODS

two clinicians assessed PTSE postoperatively in 20 patients implanted for at least three months in the STN. The resulting dataset of electroclinical tests was used to evaluate two methods of PTSE prediction. The first method was based on the volume of tissue activated (VTA) modeling and the second one was a data-driven-based method named Pyramidal tract side effect Model based on Artificial Neural network (PyMAN) developed in our laboratory. This method was based on the nonlinear correlation between the PTSE current threshold and the 3-D electrode coordinates. PTSE prediction from both methods was compared using Mann-Whitney U test.

RESULTS

1696 electroclinical tests were used to design and compare the two methods. Sensitivity, specificity, positive- and negative-predictive values were significantly higher with the PyMAN method than with the VTA-based method (P < 0.05).

CONCLUSION

the PyMAN method was more effective than the VTA-based method to predict PTSE.

SIGNIFICANCE

this data-driven tool could help the neurosurgeon in predicting adverse side effects induced by DBS during the electrode trajectory preplanning.

Image-guided preoperative prediction of pyramidal tract side effect in deep brain stimulation: proof of concept and application to the pyramidal tract side effect induced by pallidal stimulation

Deep brain stimulation of the medial globus pallidus (GPm) is a surgical procedure for treating patients suffering from Parkinson's disease. Its therapeutic effect may be limited by the presence of pyramidal tract side effect (PTSE). PTSE is a contraction time-locked to the stimulation when the current spreading reaches the motor fibers of the pyramidal tract within the internal capsule. The objective of the study was to propose a preoperative predictive model of PTSE. A machine learning-based method called PyMAN (PTSE model based on artificial neural network) accounting for the current used in stimulation, the three-dimensional electrode coordinates and the angle of the trajectory, was designed to predict the occurrence of PTSE. Ten patients implanted in the GPm have been tested by a clinician to create a labeled dataset of the stimulation parameters that trigger PTSE. The kappa index value between the data predicted by PyMAN and the labeled data was 0.78. Further evaluation studies are desirable to confirm whether PyMAN could be a reliable tool for assisting the surgeon to prevent PTSE during the preoperative planning.

Pre-frontal-insular-cerebellar modifications correlate with disgust feeling blunting after subthalamic stimulation: A positron emission tomography study in Parkinson's disease

Subthalamic nucleus (STN) deep brain stimulation (DBS) has recently advanced our understanding of the major role played by this basal ganglion in human emotion. Research indicates that STN DBS can induce modifications in all components of emotion, and neuroimaging studies have shown that the metabolic modifications correlated with these emotional disturbances following surgery are both task- and sensory input-dependent. Nevertheless, to date, these modifications have not been confirmed for all emotional components, notably subjective emotional experience, or feelings. To identify the neural network underlying the modification of feelings following STN DBS, we assessed 16 patients with Parkinson's disease before and after surgery, using both subjective assessments of emotional experience and ¹⁸ [F]fluorodeoxyglucose positron emission tomography (¹⁸ FDG-PET). The patients viewed six film excerpts intended to elicit happy, angry, fearful, sad, disgusted, and neutral feelings, and they self-rated the intensity of these feelings. After DBS, there was a significant reduction in the intensity of the disgust feeling. Correlations were observed between decreased disgust experience and cerebral glucose metabolism (FDG uptake) in the bilateral pre-frontal cortices (orbitofrontal, dorsolateral, and inferior frontal gyri), bilateral insula, and right cerebellum. We suggest that the STN contributes to the synchronization process underlying the emergence of feelings.

Improving recorded volume in mesial temporal lobe by optimizing stereotactic intracranial electrode implantation planning

PURPOSE

Intracranial electrodes are sometimes implanted in patients with refractory epilepsy to identify epileptic foci and propagation. Maximal recording of EEG activity from regions suspected of seizure generation is paramount. However, the location of individual contacts cannot be considered with current manual planning approaches. We propose and validate a procedure for optimizing intracranial electrode implantation planning that maximizes the recording volume, while constraining trajectories to safe paths.

METHODS

Retrospective data from 20 patients with epilepsy that had electrodes implanted in the mesial temporal lobes were studied. Clinical imaging data (CT/A and T1w MRI) were automatically segmented to obtain targets and structures to avoid. These data were used as input to the optimization procedure. Each electrode was modeled to assess risk, while individual contacts were modeled to estimate their recording capability. Ordered lists of trajectories per target were obtained. Global optimization generated the best set of electrodes. The procedure was integrated into a neuronavigation system.

RESULTS

Trajectories planned automatically covered statistically significant larger target volumes than manual plans [Formula: see text]. Median volume coverage was [Formula: see text] for automatic plans versus [Formula: see text] for manual plans. Furthermore, automatic plans remained at statistically significant safer distance to vessels [Formula: see text] and sulci [Formula: see text]. Surgeon's scores of the optimized electrode sets indicated that 95% of the automatic trajectories would be likely considered for use in a clinical setting.

CONCLUSIONS

This study suggests that automatic electrode planning for epilepsy provides safe trajectories and increases the amount of information obtained from the intracranial investigation.