Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Yuval Duchin, Reuben R. Shamir, Remi Patriat, Jinyoung Kim, Jerrold L. Vitek, Guillermo Sapiro, Noam Harel - Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota; Surgical Information Sciences, Minneapolis; Departments of Electrical & Computer Engineering, Computer Science, Biomedical Engineering and Math, Duke University; Department of Neurology, University of Minnesota

Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and measured the variability of the location and dimensions across movement disorder patients.

72 patients who underwent DBS surgery were scanned preoperatively on 7T MRI. Segmentations and 3D volume rendering of the STN were generated for all patients. For 21 STN-DBS cases, microelectrode recording (MER) was used to validate the segmentation. For 12 cases, we computed the correlation between the overlap of the STN and volume of tissue activated (VTA) and the monopolar review for a further validation of the model’s accuracy and its clinical relevancy.

We successfully reconstructed and visualized the STN in all patients. Significant variability was found across individuals regarding the location of the STN center of mass as well as its volume, length, depth and width. Significant correlations were found between MER and the 7T imaging-based model of the STN (r = 0.86) and VTA-STN overlap and the monopolar review outcome (r = 0.61).

The results suggest that an accurate visualization and localization of a patient-specific 3D model of the STN can be generated based on 7T MRI. The imaging-based 7T MRI STN model was validated using MER and patient’s clinical outcomes. The significant variability observed in the STN location and shape based on a large number of patients emphasizes the importance of an accurate direct visualization of the STN for DBS targeting. An accurate STN localization can facilitate postoperative stimulation parameters for optimized patient outcome.

How Amira-Avizo Software is used

The STNs of each patient were manually segmented (voxel by voxel) on the 7T data using Amira version 5.4.1 or Avizo version 9.2 software (FEI, Hillsboro, OR, USA).


We used Amira version 5.4.1 or Avizo version 9.2 software as the registration platform. For each case, a careful inspection of the registration was performed by visually assessing the alignment of visible features of the images such as borders lines, vessels, visible nuclei, etc.


The electrode 3D model was semi-automatically extracted using either Amira version 5.4.1 or Avizo version 9.2 (FEI, Hillsboro, OR, USA). Then, an exact 3D representation of the specific electrode implanted in the patient was matched with the segmentation. The 3D electrode model was generated following the dimensions provided by the vendor and included a shaft, a tip, and four contacts (in all cases the electrode model was Medtronic DBS lead 3389). The pre-operative 7T MRI and post-operative CT scan were linearly co-registered using Amira version 5.4.1 or Avizo version 9.2 software.