AbstractDuring functional MRI (fMRI) studies, blood oxygenation‐level dependent (BOLD) signal associated with neuronal activity acquired from multiple individuals are subject to the derivation of group‐averaged brain activation patterns. Unlike other cortical areas, subcortical areas such as the thalamus and basal ganglia often manifest smaller, biphasic BOLD signal that are aberrant from signals originating from cortices. Independent component analysis (ICA) can offer session/individual specific brain activation maps without a priori assumptions regarding the timing or pattern of the signal responses. The small activation loci within the subcortical areas are sparsely distributed among the subjects, and a conventional group processing method based on the general linear model (GLM) or ICA may fail to characterize the activation loci. In this article, we present an independent vector analysis (IVA) to overcome these limitations by offering an analysis of additional dependent components (compared to the ICA‐based method) that are assigned for use in the automated grouping of dependent (i.e., similar) activation patterns across subjects. The proposed IVA algorithm was applied to simulated data, and its utility was confirmed from real fMRI data employing a trial‐based hand motor task. A GLM and the group ICA of the fMRI toolbox (GIFT) were also applied for comparison. From the analysis of activation patterns within subcortical areas, in which the hemodynamic responses (HRs) often deviate from a canonical, model‐driven HR, IVA detected task‐related activation loci that were not detected through GLM and GIFT. IVA may offer a unique advantage for inferring group activation originating from subcortical areas. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 29–41, 2008