Functional Parcellation of fMRI data using multistage k-means clustering

Purpose: Functional Magnetic Resonance Imaging (fMRI) data acquired through resting-state studies have been used to obtain information about the spontaneous activations inside the brain. One of the approaches for analysis and interpretation of resting-state fMRI data require spatially and functionally homogenous parcellation of the whole brain based on underlying temporal fluctuations. Clustering is often used to generate functional parcellation. However, major clustering algorithms, when used for fMRI data, have their limitations. Among commonly used parcellation schemes, a tradeoff exists between intra-cluster functional similarity and alignment with anatomical regions. Approach: In this work, we present a clustering algorithm for resting state and task fMRI data which is developed to obtain brain parcellations that show high structural and functional homogeneity. The clustering is performed by multistage binary k-means clustering algorithm designed specifically for the 4D fMRI data. The results from this multistage k-means algorithm show that by modifying and combining different algorithms, we can take advantage of the strengths of different techniques while overcoming their limitations. Results: The clustering output for resting state fMRI data using the multistage k-means approach is shown to be better than simple k-means or functional atlas in terms of spatial and functional homogeneity. The clusters also correspond to commonly identifiable brain networks. For task fMRI, the clustering output can identify primary and secondary activation regions and provide information about the varying hemodynamic response across different brain regions. Conclusion: The multistage k-means approach can provide functional parcellations of the brain using resting state fMRI data. The method is model-free and is data driven which can be applied to both resting state and task fMRI.