Objective: To compare the specificity and sensitivity of fractional amplitude of low-frequency fluctuation (fALFF), regional homogeneity (Reho) and functional connectivity (FC) in resting-state fMRI data analysis. Methods: Resting-state fMRI were acquired in 10 subacute pontine infarction patients and 10 normal controls. The data were analyzed with different methods. The activations of resting-state networks (RSN) of the patients were taken and compared with normal controls, and then the increased and decreased brain regions were demonstrated. Results: In fALFF and Reho, the RSN of patients mainly distributed in posterior default mode network (pDMN) and primary visual cortex. In FC, the RSN mainly distributed in DMN. Compared with normal controls, there was no effect in Reho, and there were different results in fALFF and FC. The results in FC were influenced by different ROI. Conclusion: fALFF and Reho are methods for local activity (segregation), FC are for integration of distinct brain regions. For these data, the sensitivity of methods from bad to good is Reho, fALFF, FC. ROI chosen in FC has significant impact on the sensitivity during group analysis, based on the functional activation maps from it's own data is better than previous literature. Copyright © 2013 by the Press of Chinese Journal of Medical Imaging Technology.