A vendor-neutral functional MRI acquisition protocol for multi-site studies

We present an open, vendor-neutral BOLD SMS-EPI protocol tailored for multi-site fMRI studies, intended as a drop-in replacement for conventional vendor-specific acquisition and reconstruction pipelines. Built on Pulseq—an emerging standard for cross-platform MRI pulse sequence development—our protocol ensures identical SMS-EPI pulse sequences and image reconstruction across scanner vendors. This provides, for the first time, known and consistent experimental conditions across sites and scanner software versions. We begin by reviewing the current capabilities of the Pulseq framework, including vendor support and safety considerations. We then detail our SMS-EPI implementation and demonstrate its performance using resting-state fMRI pilot data from healthy volunteers, showing reduced site variance compared to corresponding vendor protocols on Siemens and GE scanners. To support adoption, we provide practical resources to help researchers integrate Pulseq fMRI into their studies, including example text for grant proposals and IRB submissions. These resources are freely available at https://github.com/HarmonizedMRI/Functional (https://github.com/HarmonizedMRI/Functional). Our vision is for Pulseq fMRI to become the standard for multi-site research, enabling more reproducible science and serving as a reference for the development of novel acquisition and reconstruction methods.