BOLDsωimsuite: A new software suite for forward modeling of the BOLD fMRI signal

Many methods for the forward modeling of the blood-oxygenation level-dependent (BOLD) effect have been created and analyzed to elucidate the mechanisms of BOLD functional MRI (fMRI) techniques and to expand on the potential of the transverse relaxation time (T₂*) in quantitative MRI. Simulations of this nature can be difficult to implement without prior experience, and differences made by methodological choices can be unclear, which provides a significant barrier of entry into the field. In this paper, we present BOLDsωimsuite, a toolbox for forward modeling of the BOLD effect, which collects many of the principal methods used in the literature into a single coherent package. Implemented as a Python package, simulations are made using scripts by combining various simulation components, thereby providing flexibility in methodological choices. The goal of this toolbox is to provide an open-source, reproducible simulation software suite that is adaptable for different MRI applications, and to which additional features can be added by the user with relative ease. This paper first provides an overview of the methods available in the package and how these methods can be constructed from the toolbox's modular code components. Then, a brief theoretical explanation of each simulation component is given, supported by the relevant contributors. Next, sample simulations and analyzes that can be created using the package are presented to display its features. Finally, recommendations regarding computational requirements are included to help users choose the best simulation methods to fit their needs. This package has many use cases and significantly reduces methodological barriers to forward modeling. It can also be a good learning tool for MR physics as well as a powerful tool to promote reproducible science.