© 2015 IEEE. This paper presents a prediction framework of brain subcortical structures which are invisible on clinical low-field MRI, learning detailed information from ultrahigh-field MR training data. Volumetric segmentation of Deep Brain Stimulation (DBS) structures within the Basal ganglia is a prerequisite process for reliable DBS surgery. While ultrahigh-field MR imaging (7 Tesla) allows direct visualization of DBS targeting structures, such ultrahigh-fields are not always clinically available, and therefore the relevant structures need to be predicted from the clinical data. We address the shape prediction problem with a regression forest, non-linearly mapping predictors to target structures with high confidence, exploiting ultrahigh-field MR training data. We consider an application for the subthalamic nucleus (STN) prediction as a crucial DBS target. Experimental results on Parkinson's patients validate that the proposed approach enables reliable estimation of the STN from clinical 1.5T MRI.