Accessible and reproducible mesoscale fMRI at 5.0 T: A Pulseq-based open framework for human laminar mapping

Abstract Mesoscale, layer-specific functional MRI (fMRI) enables noninvasive access to cortical microcircuitry, yet widespread adoption has been constrained by a reliance on ultra-high field (≥7.0 T) systems and proprietary pulse sequences. To bridge this gap and enhance accessibility, we developed an open-source framework at 5.0 T for mapping laminar brain activity. This framework integrates a Pulseq-based 3D vascular space occupancy (VASO) sequence with an end-to-end data acquisition and analysis pipeline. At matched sub-millimeter resolution (0.8 mm in-plane), the Pulseq-based 3D implementation increased slab coverage by ∼1.82-fold and improved temporal signal-to-noise ratio by ∼1.50-fold relative to a vendor-provided 2D-VASO sequence. Validated using a finger-tapping paradigm, individual cerebral blood volume-weighted (VASO) laminar activation profiles consistently revealed the canonical “double-peak” pattern, with distinct superficial and deep peaks in the primary motor cortex. These profiles exhibited excellent cross-visit reliability (r = 0.80), and peak depths showed good spatial reliability (ICC = 0.69 for deep layers; ICC = 0.58 for superficial layers). Between-subject reproducibility was high (r = 0.86). Deploying the identical Pulseq protocol at an independent imaging site reproduced the characteristic double-peak laminar profiles (r = 0.63). At the group level, 5.0 T laminar profiles closely matched established 7.0 T findings, robustly resolving both deep and superficial peaks despite the lower field strength. Notably, for each participant, a single 13-minute VASO run was sufficient to resolve reliable laminar activation patterns that exhibited high consistency with multi-run averages (r = 0.78), highlighting the potential for high-throughput population studies or clinical research settings. The Pulseq-based 3D VASO sequence file, image reconstruction pipeline, and data analysis scripts are openly available to facilitate the adoption of this framework. This work establishes a practical route towards more accessible and reproducible mesoscale fMRI for studying human laminar functional architecture.