Deep-learning based fully automatic segmentation of the globus pallidus interna and externa using ultra-high 7 Tesla MRI

Oren Solomon, Tara Palnitkar, Re'mi Patriat, Henry Braun, Joshua Aman, Michael C. Park, Jerrold Vitek, Guillermo Sapiro, Noam Harel

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Deep brain stimulation (DBS) surgery has been shown to dramatically improve the quality of life for patients with various motor dysfunctions, such as those afflicted with Parkinson's disease (PD), dystonia, and essential tremor (ET), by relieving motor symptoms associated with such pathologies. The success of DBS procedures is directly related to the proper placement of the electrodes, which requires the ability to accurately detect and identify relevant target structures within the subcortical basal ganglia region. In particular, accurate and reliable segmentation of the globus pallidus (GP) interna is of great interest for DBS surgery for PD and dystonia. In this study, we present a deep-learning based neural network, which we term GP-net, for the automatic segmentation of both the external and internal segments of the globus pallidus. High resolution 7 Tesla images from 101 subjects were used in this study; GP-net is trained on a cohort of 58 subjects, containing patients with movement disorders as well as healthy control subjects. GP-net performs 3D inference in a patient-specific manner, alleviating the need for atlas-based segmentation. GP-net was extensively validated, both quantitatively and qualitatively over 43 test subjects including patients with movement disorders and healthy control and is shown to consistently produce improved segmentation results compared with state-of-the-art atlas-based segmentations. We also demonstrate a postoperative lead location assessment with respect to a segmented globus pallidus obtained by GP-net.

Original languageEnglish (US)
Pages (from-to)2862-2879
Number of pages18
JournalHuman Brain Mapping
Issue number9
Early online dateMar 18 2021
StatePublished - Jun 15 2021

Bibliographical note

Funding Information:
This study was funded by the following National Institution of Health Grants: R01 NS081118, R01 NS113746, P50 NS098753, P30 NS076408, and P41 EB027061. Additional support by NSF (GS) and Department of Defense (GS) is also acknowledged.

Publisher Copyright:
© 2021 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.


  • 7 Tesla magnetic resonance imaging
  • Parkinson's disease
  • convolutional neural network
  • deep brain stimulation
  • deep-learning
  • globus pallidus
  • patient-specific
  • segmentation

Center for Magnetic Resonance Research (CMRR) tags

  • IRP
  • NM
  • P41


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