Magnetization transfer weighted EPI facilitates cortical depth determination in native fMRI space

Abstract

The increased availability of ultra-high field scanners provides an opportunity to perform fMRI at sub-millimeter spatial scales and enables in vivo probing of laminar function in the human brain. 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 are used as MT preparation, with a flexible duration (several to tens of milliseconds), which can be applied before each EPI segment without constraining the acquisition length (segment or slice number). The method’s feasibility was demonstrated at 7T for coverage of either a small slab or the near-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. This MT-weighted EPI image allows an automatic reconstruction of the cortical surface to support laminar analysis in native fMRI space, obviating the need for distortion correction and registration.

Acquisition and processing methods of whole-brain layer-fMRI VASO and BOLD: The Kenshu dataset

“…In ongoing sequence development projects, Yuhui Chai is taking advantage of the developed k-space acquisition procedures (acquisition protocols and sampling patterns) for whole-brain sub-millimeter EPI acquisition with MT-prepared and VAPER prepared contrasts (Chai et al 2021).…”

“…While layer-fMRI and VASO is still in the process of becoming an established standard neuroscience tool, at recent BrainHack events(Gau et al 2021), Remi Gau has used the Kenshu dataset to exemplify how one could store layer-fMRI VASO data in an extended BIDS In ongoing sequence development projects, Yuhui Chai is taking advantage of the developed k-space acquisition procedures (acquisition protocols and sampling patterns) for whole-brain sub-millimeter EPI acquisition with MT-prepared and VAPER prepared contrasts(Chai et al 2021).• Preliminary accounts of this dataset have been used to implement, calibrate, and validate resolution biases in layerification algorithms (Figure…”

Submillimeter fMRI Acquisition Techniques for Detection of Laminar and Columnar Level Brain Activation

“…42 Therefore, to acquire an anatomical scan using EPI, a contrast preparation module, such as inversion or magnetization transfer, is used, which can deliver the magnetization-prepared, rapid GE (MPRAGE)-like T 1 contrast. 42,95 In this way, the T 1weighted, anatomical EPI scan has distortions identical to the fMRI data, resulting in errorless co-registration between the anatomical and functional scans. 95 The feasibility of using this technique for subcortical fMRI has been demonstrated previously.…”

“…The definition of the cortical boundaries from the anatomical scan is particularly important for subcortical functional analysis to enable the location of cortical layers or columns to be determined. However, a typical EPI protocol used in fMRI does not have sufficient structural contrast to segment the cortical regions out of other tissue components 42 . Therefore, to acquire an anatomical scan using EPI, a contrast preparation module, such as inversion or magnetization transfer, is used, which can deliver the magnetization‐prepared, rapid GE (MPRAGE)‐like T 1 contrast 42,95 .…”

“…However, a typical EPI protocol used in fMRI does not have sufficient structural contrast to segment the cortical regions out of other tissue components 42 . Therefore, to acquire an anatomical scan using EPI, a contrast preparation module, such as inversion or magnetization transfer, is used, which can deliver the magnetization‐prepared, rapid GE (MPRAGE)‐like T 1 contrast 42,95 . In this way, the T 1 ‐weighted, anatomical EPI scan has distortions identical to the fMRI data, resulting in errorless co‐registration between the anatomical and functional scans 95 …”