Provides a set of python scripts for deriving a whole brain parcellation of functional magnetic resonance imaging (fMRI) data. The resulting regions are suitable for use as regions of interest (ROIs) in fMRI data analysis. The pyClusterROI method employs a spatially-constrained normalized-cut spectral clustering algorithm to generate individual-level and group-level parcellations. The spatial constraint is imposed to ensure that the resulting ROIs are spatially coherent, i.e. the voxels in the resulting ROIs are connected. Using this package, clustering can be performed based on either the temporal correlation between voxel time courses, the spatial correlation between whole brain functional connectivity maps generated from each voxel time course, or a by spatial distance.