Biology subjects

Oostenveld, R.

Publications and source records attributed to Oostenveld, R..

4 recordsLinked to original sources

bioRxiv2018

Lead-DBS v2: Toward 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 patients 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 method of choice.\n\nThis 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.

neuroscience↗

bioRxiv2017

Integrated analysis of anatomical and electrophysiological human intracranial data

The exquisite spatiotemporal precision of human intracranial EEG recordings (iEEG) permits characterizing neural processing with a level of detail that is inaccessible to scalp-EEG, MEG, or fMRI. However, the same qualities that make iEEG an exceptionally powerful tool also present unique challenges. Until now, the fusion of anatomical data (MRI and CT images) with the electrophysiological data and its subsequent analysis has relied on technologically and conceptually challenging combinations of software. Here, we describe a comprehensive protocol that addresses the complexities associated with human iEEG, providing complete transparency and flexibility in the evolution of raw data into illustrative representations. The protocol is directly integrated with an open source toolbox for electrophysiological data analysis (FieldTrip). This allows iEEG researchers to build on a continuously growing body of scriptable and reproducible analysis methods that, over the past decade, have been developed and employed by a large research community. We demonstrate the protocol for an example complex iEEG data set to provide an intuitive and rapid approach to dealing with both neuroanatomical information and large electrophysiological data sets. We explain how the protocol can be largely automated, taking under an hour to complete, and readily adjusted to iEEG data sets with other characteristics.

neuroscience↗

bioRxiv2017

Reconstruction of resting-state networks from macaqueelectrocorticographic data

The discovery of haemodynamic (BOLD-fMRI) resting-state networks (RSNs) has brought about a fundamental shift in our thinking about the role of intrinsic brain activity. The electrophysiological underpinnings of RSNs remain largely elusive and it has been shown only recently that electrophysiological cortical rhythms are organized into RSNs. Most electrophysiological studies into RSNs use magnetoencephalography (MEG) or electroencephalography (EEG), which limits the spatial scale on which RSNs can be investigated. Due to their close proximity to the cortical surface, electroencephalographic (ECoG) recordings can potentially provide a more detailed picture of the functional organization of resting-state cortical rhythms. In this study we propose using source-space independent component analysis for identifying generators of resting-state cortical rhythms as recorded with ECoG and reconstructing their network structure. Their network structure is characterized by two kinds of connectivity: instantaneous correlations between band-limited amplitude envelopes and oscillatory phase-locking. Using simulated data, we find that the reconstruction of oscillatory phase-locking is more challenging than that of amplitude correlations, particularly for low signal-to-noise levels. Specifically, phase-lags can both be over- and underestimated as a consequence of first-order and higher-order volume-conduction effects, which troubles the interpretation of interaction measures based on imaginary phase-locking or coherence. The methodology is applied to resting-state beta (15-30 Hz) rhythms within the motor system of a macaque monkey and leads to the identification of a functional network of seven cortical generators that are distributed across the sensorimotor system. The spatial extent of the identified generators, together with consistent phase-lags, suggests that these rhythms can be viewed as being spatially continuous with complex dynamics including traveling waves. Our findings illustrate the level of spatial detail attainable with source-projected ECoG and motivates wider use of the methodology for studying resting-state as well as event-related cortical dynamics in macaque and human.

neuroscience↗

bioRxiv2017

MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG provides direct measurement of brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS has provided a solution to structure the organization of magnetic resonance imaging (MRI) data, which nature and acquisition parameters are different. Despite the lack of standard data format for MEG, MEG-BIDS is a principled solution to store, organize and share the typically-large data volumes produced. It builds on BIDS for MRI, and therefore readily yields a multimodal data organization by construction. This is particularly valuable for the anatomical and functional registration of MEG source imaging with MRI. With MEG-BIDS and a growing range of software adopting the standard, the MEG community has a solution to minimize curation overheads, reduce data handling errors and optimize usage of computational resources for analytics. The standard also includes well-defined metadata, to facilitate future data harmonization and sharing efforts.

neuroscience↗