fMRI of the Basal Ganglia at 7T using single- and multi-echo protocols
The Basal Ganglia (BG) play a crucial role in cognition and neural diseases. Studying their functioning could help elucidate the neural underpinnings of therapies such as deep-brain stimulation and cognitive processes such as response inhibition. Functional Magnetic Resonance Imaging (fMRI) of the BG with high specificity, however, is challenging, because the nuclei are small and variable in their anatomical location. Furthermore, the magnetic properties of these iron-rich structures are considerably different from cortical regions, rendering "standard" fMRI protocols intended for mapping the cortex sub-optimal for investigating the Basal Ganglia.
We therefore optimized a conventional single-echo fMRI protocol accordingly and conducted a study at a field strength of 7 Tesla using a so-called "stop-signal reaction" task. The experiments resulted in significant task-related activity in the sub-cortical BG nuclei which was not the case for fMRI protocols not optimized for mapping the Basal Ganglia. Imaging parameters adjusted to the magnetic properties of the Basal Ganglia and a sufficient Signal-to-Noise Ratio (SNR) are therefore necessary to functionally image those small sub-cortical structures. In order to simultaneously map the cortical areas involved in the stop-signal reaction task, we further adjusted a multi-echo fMRI protocol and compared it to the first single-echo approach. Contrary to our expectations, however, both protocols provided a similar sensitivity across the brain at 7 Tesla as shown in the figure below. Here, activation maps for the three main contrasts of the "stop-signal reaction" task for both the single-echo and optimally combined (OC) multi-echo data are displayed. (Contours indicate the regions of interest: right Inferior Frontal Gyrus in white, Striatum in blue, Globus Pallidus Externus and Globus Pallidus Internus in dark and light green, respectively, and Subthalamic Nucleus in light blue).
The apparent discrepancy with theoretical predictions can be explained by the necessary use of accelerated imaging. In order to optimize a multi-echo fMRI protocol for detecting cortical and sub-cortical neural activity, a significant amount of signal under-sampling must be performed. This, however, decreased the intrinsic SNR of the sequence, especially at the position of the BG in the deeper parts of the brain. The benefits of using multiple-echo protocols are thus counterbalanced by this loss in SNR. Therefore, when studying small, subcortical nuclei in relation to cortical areas, the used fMRI protocol has to be carefully adjusted with respect to its region of interest and the necessary signal under-sampling.