We modified a parcellation method to map the motor, limbic and associative territories within the subthalamic nucleus (STN). We further evaluated whether a remapping of the STN connectivity exists in Parkinson’s disease (PD) patients. Resting-state fMRI data were analyzed using independent component analysis and general linear model. In both groups, the motor area was identified in the posterior zone, while the limbic zone was more anteriorly located. The motor connections were altered in the PD patients. Our approach could be used for functional parcellations and for remapping of functional connectivity due to disease in brain areas with heterogeneous connectivity patterns.