High-resolution Functional Magnetic Resonance Imaging Methods for Human Midbrain

Summary

This article describes techniques to perform high-resolution functional magnetic resonance imaging with 1.2 mm sampling in human midbrain and subcortical structures using a 3T scanner. Use of these techniques to resolve topographic maps of visual stimulation in the human superior colliculus (SC) is given as an example.

Abstract

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon measuring activity on the surface of cerebral cortex rather than in subcortical regions such as midbrain and brainstem. Subcortical fMRI must overcome two challenges: spatial resolution and physiological noise. Here we describe an optimized set of techniques developed to perform high-resolution fMRI in human SC, a structure on the dorsal surface of the midbrain; the methods can also be used to image other brainstem and subcortical structures.

High-resolution (1.2 mm voxels) fMRI of the SC requires a non-conventional approach. The desired spatial sampling is obtained using a multi-shot (interleaved) spiral acquisition¹. Since, T₂* of SC tissue is longer than in cortex, a correspondingly longer echo time (T_E ~ 40 msec) is used to maximize functional contrast. To cover the full extent of the SC, 8-10 slices are obtained. For each session a structural anatomy with the same slice prescription as the fMRI is also obtained, which is used to align the functional data to a high-resolution reference volume.

In a separate session, for each subject, we create a high-resolution (0.7 mm sampling) reference volume using a T₁-weighted sequence that gives good tissue contrast. In the reference volume, the midbrain region is segmented using the ITK-SNAP software application². This segmentation is used to create a 3D surface representation of the midbrain that is both smooth and accurate³. The surface vertices and normals are used to create a map of depth from the midbrain surface within the tissue⁴.

Functional data is transformed into the coordinate system of the segmented reference volume. Depth associations of the voxels enable the averaging of fMRI time series data within specified depth ranges to improve signal quality. Data is rendered on the 3D surface for visualization.

In our lab we use this technique for measuring topographic maps of visual stimulation and covert and overt visual attention within the SC¹. As an example, we demonstrate the topographic representation of polar angle to visual stimulation in SC.

Protocol

1. Polar-angle Topography Stimulus and Psychophysics

To obtain a polar-angle retinotopic map in the SC, we use a 90° wedge of moving dots as the stimulus (eccentricity 2-9° of visual angle, mean dot-speed 4° / sec) (Fig. 1). It is known that activity in the SC is enhanced by applying covert attention⁵, hence we use an attention task in our paradigm to increase available signal. On each 2 s trial, subjects are instructed to covertly attend to the entire wedge and perform a speed discrimination task while maintaining fixation. The wedge is divided into 2 × 3 virtual sectors with dots in one of the sectors, randomly c....

Discussion

Our acquisition and data-analysis techniques enable the measurement of neural activity in subcortical human brain structures at high resolution (1.2 mm voxels). The 3-shot spiral acquisition reduces the physiological noise that is particularly detrimental to fMRI measurements around the midbrain. In addition, our laminar segmentation of the tissue allows us to perform depth averaging of the data that helps improve the SNR. We have used these methods to show precise polar-angle topographic maps of visual stimulation and c.......