In recent years, ultra-high field functional MRI has allowed researchers to study cortical activity at high spatiotemporal resolution. Advancements in technology have made it possible to perform fMRI of cortical laminae, which is crucial for understanding and mapping of local circuits and overall brain function. Unlike invasive electrophysiology, fMRI provides a non-invasive approach to studying human and animal brain function. However, achieving high spatial resolution has often meant sacrificing temporal resolution. In contrast, line-scanning fMRI maintains both high spatial and temporal resolution, and has been successfully applied to animals to detect laminar differences of the hemodynamic response. Although this method has been extended to human brain imaging in initial studies, staying within SAR safety limits while maintaining a well-defined saturation profile at a short TR is a major challenge. We present a method for gradient-echo-based human line-scanning that uses four saturation regions to achieve a line with narrow FWHM (3.9 mm) at high spatiotemporal resolution (voxel size 0.39 x 3.0 x 3.0 mm 3 , TR = 250 ms). We demonstrate its use for laminar fMRI by measuring laminar time courses in the hand knob of the primary human motor cortex during a finger-tapping task. Our findings indicate differences in the onset and temporal characteristics of the hemodynamic response across cortical layers. Deeper layers exhibited distinct temporal dynamics compared with the gray matter near the cortical surface. Specifically, the BOLD response reached 95% of the maximum amplitude earlier than the superficial layers, and demonstrated a faster return to baseline after stimulus offset. We demonstrate that line-scanning fMRI offers a valuable tool for investigating recordings at a very high temporal and spatial resolution and could help advance our understanding of the mechanistic nature of the BOLD response.

Functional MRI (fMRI) time series are inherently susceptible to the influence of respiratory variations. While many studies treat respiration as a source of noise in fMRI, this study employs natural respiratory variations during high resolution (0.8 mm) fMRI at 7T to formulate a respiration effect related map and then use this map to reduce macrovascular bias for a more laminar-specific fMRI measurement. Our results indicate that respiratory-related signal changes are modulated by breath phase (breathing in/out or in the transition between breath in and out) during fMRI acquisition, with distinct patterns across various brain regions. We demonstrate that respiration maps generated from normal fMRI runs, such as task-oriented sessions, closely resemble those from deep-breath and breath-hold experiments. These maps show a significant correlation with the macro-vasculature automatically segmented based on susceptibility weighted imaging (SWI) and quantitative susceptibility mapping (QSM) images. Most crucially, by removing voxels most responsive to respiratory variations, we can refine high-resolution fMRI measurements to be more layer-specific, improving the accuracy of laminar fMRI analysis.

Neuroscientific investigations at the cortical layer level not only enrich our knowledge of cortical micro-circuitry in vivo, but also help bridge the gap between macroscopic (e.g., conventional fMRI, behavior) and microscopic (e.g., extracellular recordings) measures of brain function. While laminar fMRI studies have extensively explored the evoked cortical response in multiple subsystems, the investigation of the laminar component of functional networks throughout the entire brain has been hindered due to constraints in high-resolution layer-fMRI imaging methodologies. Our study addresses this gap by introducing an innovative layer-specific 3D VAPER (integrated VASO and Perfusion contrast) technique in humans at 7 T, for achieving fMRI at high resolution (800 µm isotropic), high specificity (not biased toward unspecific vein signals as BOLD), high sensitivity (robust measurement at submillimeter resolution), high spatial accuracy (analysis in native fMRI space), near-whole-brain coverage (cerebellum not included), and eventually extending layer fMRI to more flexible connectivity-based experiment designs. To demonstrate its effectiveness, we collected 0.8-mm isotropic fMRI data during both resting-state and movie-watching scenarios, established a layer-specific functional connectivity analysis pipeline from individual to group levels, and explored the role of different cortical layers in maintaining functional networks. Our results revealed distinct layer-specific connectivity patterns within the default mode, somatomotor, and visual networks, as well as at the global hubness level. The cutting-edge technique and insights derived from our exploration into near-whole-brain layer-specific connectivity provide unparalleled understanding of the organization principles and underlying mechanisms governing communication between different brain regions.