Table 1.

Potential confounding factors affecting BOLD signal generation in MS studies and strategies to overcome them.

Source of fMRI signal	Confounding factors	Strategy to control for confounding factors
Neural signalling	Disease-related or intervention-related increases or decreases in brain activity	Simultaneous or delayed electrophysiological recording
Neurovascular coupling	Disease-related or intervention-related effect on vascular response to changes of neural activity	Measure vascular reactivity (for example, with carbon dioxide challenge)
Vascular compartment	Disease-related or intervention-related differences in baseline perfusion levels	Measure baseline perfusion Measure perfusion response to a task