**Abstract**

Resting-state fMRI has been widely applied in clinical research. Brain networks constructed by functional connectivity can reveal alterations related to disease and treatment. One of the major concerns of brain network application under clinical situations is how to analyze groups of data to find the potential biomarkers that can aid in diagnosis. In this paper, we briefly review common methods to construct brain networks from resting-state fMRI data, including different ways of the node definition and edge calculation. We focus on using a brain atlas to define nodes and estimate edges by static and dynamic functional connectivity. The directed connectivity method is also mentioned. We then discuss the challenges and pitfalls when analyzing groups of brain networks, including functional connectivity alterations, graph theory attributes analysis, and network-based statistics. Finally, we review the clinical application of resting-state fMRI in neurorehabilitation of spinal cord injury patients and stroke patients, the research on the mechanism and early diagnosis of neurodegenerative diseases, such as multiple system atrophy, as well as the research on brain functional network alteration of glioma patients.

**Keywords:** resting-state fMRI, brain networks, graph theory attributes, dynamic functional connectivity, network-based statistics, neurorehabilitation, multiple system atrophy, glioma
