Zeffiro user interface for electromagnetic brain imaging: a GPU accelerated FEM tool for forward and inverse computations in Matlab

Abstract

This article introduces the Zeffiro interface (ZI) for brain imaging. ZI is an attempt to provide a simple and accessible and multimodal open source platform for FEM based forward and inverse computations. Zeffiro is Italian for a 'gentle breeze'. ZI has been implemented for the Matlab environment. It allows one to (1) generate the FE mesh for a given multi-layer head model, (2) form a basis for computing a LF matrix and inverting a given set of measurements, and (3) to visualize the reconstructions on the FE mesh. To tackle the issue of the high computational cost, ZI uses graphics processing unit (GPU) acceleration for each of the processing stages (1)-(3). In its current configuration, ZI includes forward solvers for E/MEG and linearized EIT LF matrices and and a set of inverse solvers utilizing the hierarchical Bayesian model (HBM). In this paper, we describe the mathematics behind the ZI, describe the principle operations and usage of ZI, concentrating especially on EEG/MEG, and introduce some central points for the developer perspective. We also give examples of computing times, and analyze numerically how the inversion parameters should be selected, when inverting brain activity with HBM.