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

Background and Objectives This article introduces the Zeffiro interface (ZI) for brain imaging. Zeffiro is Italian for a 'gentle breeze'. ZI is an attempt to provide a simple and accessible and multimodal open source platform for Finite Element Method based forward and inverse computations in the Matlab environment. Methods It allows one to (1) generate the finite element mesh for a given multi-layer head model, (2) form a basis for computing a lead field matrix and inverting a given set of measurements, and (3) to visualize the reconstructions on the finite element mesh. ZI uses graphics processing unit acceleration for each of the processing stages (1)-(3) to tackle the issue of the high computational cost. In its current configuration, ZI includes forward solvers for electro-/magnetoencephalography and linearized electrical impedance tomography as well as a set of inverse solvers utilizing the hierarchical Bayesian model (HBM). Results GPU acceleration was found to be necessary, specifically, in the generation of the FE mesh and the evaluation of the LF matrix in order to achieve a feasibly short computation time. Computed examples of reconstructions and a guideline for parameter selection in HBM are given. Conclusions In this paper, we describe the mathematics behind the ZI, describe the principal operations and usage 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.