Open data for this project: https://osf.io/s4bqe/?view_only=dd8a1142ecd74d708526476b7776b717
Processing code for this project: https://github.com/yuhuichai/MT3DEPI
Abstract: The increased availability of ultra-high field scanners provides the opportunity to perform fMRI at sub-millimeter spatial scales and is starting to enable the probing of laminar function in the human brain in vivo. In most previous studies, the definition of cortical layers, or depths, is based on an anatomical reference image that is collected by a different acquisition sequence and exhibits different geometric distortion compared to the functional images. Here, we propose to generate the anatomical image with the fMRI acquisition technique by incorporating magnetization transfer (MT) weighted imaging. Small flip angle binomial pulse trains were used as MT preparation, with a flexible duration (several to tens of milliseconds), which can be applied before each EPI-based fMRI readout with no limitation of coverage. The method’s feasibility was demonstrated at 7T for coverage of either a few slices or the whole brain at 0.8 mm isotropic resolution. Tissue contrast was found to be similar to that obtained with a state-of-art anatomical reference based on MP2RAGE (3D Magnetization-Prepared 2 Rapid Acquisition Gradient Echo). This MT-weighted EPI images allow an automatic cortical surface reconstruction to support laminar analysis in native fMRI space, obviating the need for distortion correction and registration.