Dataset Information

Electric field calculations in brain stimulation based on finite elements: an optimized processing pipeline for the generation and usage of accurate individual head models.

ABSTRACT: The need for realistic electric field calculations in human noninvasive brain stimulation is undisputed to more accurately determine the affected brain areas. However, using numerical techniques such as the finite element method (FEM) is methodologically complex, starting with the creation of accurate head models to the integration of the models in the numerical calculations. These problems substantially limit a more widespread application of numerical methods in brain stimulation up to now. We introduce an optimized processing pipeline allowing for the automatic generation of individualized high-quality head models from magnetic resonance images and their usage in subsequent field calculations based on the FEM. The pipeline starts by extracting the borders between skin, skull, cerebrospinal fluid, gray and white matter. The quality of the resulting surfaces is subsequently improved, allowing for the creation of tetrahedral volume head meshes that can finally be used in the numerical calculations. The pipeline integrates and extends established (and mainly free) software for neuroimaging, computer graphics, and FEM calculations into one easy-to-use solution. We demonstrate the successful usage of the pipeline in six subjects, including field calculations for transcranial magnetic stimulation and transcranial direct current stimulation. The quality of the head volume meshes is validated both in terms of capturing the underlying anatomy and of the well-shapedness of the mesh elements. The latter is crucial to guarantee the numerical robustness of the FEM calculations. The pipeline will be released as open-source, allowing for the first time to perform realistic field calculations at an acceptable methodological complexity and moderate costs.

SUBMITTER: Windhoff M

PROVIDER: S-EPMC6870291 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Electric field calculations in brain stimulation based on finite elements: an optimized processing pipeline for the generation and usage of accurate individual head models.

Windhoff Mirko M Opitz Alexander A Thielscher Axel A

Human brain mapping 20111123 4

The need for realistic electric field calculations in human noninvasive brain stimulation is undisputed to more accurately determine the affected brain areas. However, using numerical techniques such as the finite element method (FEM) is methodologically complex, starting with the creation of accurate head models to the integration of the models in the numerical calculations. These problems substantially limit a more widespread application of numerical methods in brain stimulation up to now. We ...[more]

PMID: 22109746

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Project description:Progress in the development of GPU-accelerated free energy simulation software has enabled practical applications on complex biological systems and fueled efforts to develop more accurate and robust predictive methods. In particular, this work re-examines concerted (a.k.a., one-step or unified) alchemical transformations commonly used in the prediction of hydration and relative binding free energies (RBFEs). We first classify several known challenges in these calculations into three categories: endpoint catastrophes, particle collapse, and large gradient-jumps. While endpoint catastrophes have long been addressed using softcore potentials, the remaining two problems occur much more sporadically and can result in either numerical instability (i.e., complete failure of a simulation) or inconsistent estimation (i.e., stochastic convergence to an incorrect result). The particle collapse problem stems from an imbalance in short-range electrostatic and repulsive interactions and can, in principle, be solved by appropriately balancing the respective softcore parameters. However, the large gradient-jump problem itself arises from the sensitivity of the free energy to large values of the softcore parameters, as might be used in trying to solve the particle collapse issue. Often, no satisfactory compromise exists with the existing softcore potential form. As a framework for solving these problems, we developed a new family of smoothstep softcore (SSC) potentials motivated by an analysis of the derivatives along the alchemical path. The smoothstep polynomials generalize the monomial functions that are used in most implementations and provide an additional path-dependent smoothing parameter. The effectiveness of this approach is demonstrated on simple yet pathological cases that illustrate the three problems outlined. With appropriate parameter selection, we find that a second-order SSC(2) potential does at least as well as the conventional approach and provides vast improvement in terms of consistency across all cases. Last, we compare the concerted SSC(2) approach against the gold-standard stepwise (a.k.a., decoupled or multistep) scheme over a large set of RBFE calculations as might be encountered in drug discovery.

Dataset Information

Electric field calculations in brain stimulation based on finite elements: an optimized processing pipeline for the generation and usage of accurate individual head models.

Publications

Electric field calculations in brain stimulation based on finite elements: an optimized processing pipeline for the generation and usage of accurate individual head models.

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