Purpose: Deep brain stimulation (DBS) is an interventional treatment for some neurological and neurodegenerative diseases. For example, in Parkinson’s disease, DBS electrodes are positioned at particular locations within the basal ganglia to alleviate the patient’s motor symptoms. These interventions depend greatly on a preoperative planning stage in which potential targets and electrode trajectories are identified in a preoperative MRI. Due to the small size and low contrast of targets such as the subthalamic nucleus (STN), their segmentation is a difficult task. Machine learning provides a potential avenue for development, but it has difficulty in segmenting such small structures in volumetric images due to additional problems such as segmentation class imbalance.

Approach: We present a two-stage separable learning workflow for STN segmentation consisting of a localization step that detects the STN and crops the image to a small region and a segmentation step that delineates the structure within that region. The goal of this decoupling is to improve accuracy and efficiency and to provide an intermediate representation that can be easily corrected by a clinical user. This correction capability was then studied through a human–computer interaction experiment with seven novice participants and one expert neurosurgeon.

Results: Our two-step segmentation significantly outperforms the comparative registration-based method currently used in clinic and approaches the fundamental limit on variability due to the image resolution. In addition, the human–computer interaction experiment shows that the additional interaction mechanism allowed by separating STN segmentation into two steps significantly improves the users’ ability to correct errors and further improves performance.

Conclusions: Our method shows that separable learning not only is feasible for fully automatic STN segmentation but also leads to improved interactivity that can ease its translation into clinical use.