title: PyDBS: an automated image processing workflow for deep brain stimulation surgery.
abstract: OBJECTIVE
  Deep brain stimulation (DBS) is a surgical procedure for treating motor-related neurological disorders. DBS clinical efficacy hinges on precise surgical planning and accurate electrode placement, which in turn call upon several image processing and visualization tasks, such as image registration, image segmentation, image fusion, and 3D visualization. These tasks are often performed by a heterogeneous set of software tools, which adopt differing formats and geometrical conventions and require patient-specific parameterization or interactive tuning. To overcome these issues, we introduce in this article PyDBS, a fully integrated and automated image processing workflow for DBS surgery.
  
  
  METHODS
  PyDBS consists of three image processing pipelines and three visualization modules assisting clinicians through the entire DBS surgical workflow, from the preoperative planning of electrode trajectories to the postoperative assessment of electrode placement. The system's robustness, speed, and accuracy were assessed by means of a retrospective validation, based on 92 clinical cases.
  
  
  RESULTS
  The complete PyDBS workflow achieved satisfactory results in 92 % of tested cases, with a median processing time of 28 min per patient.
  
  
  CONCLUSIONS
  The results obtained are compatible with the adoption of PyDBS in clinical practice.
authors.affiliation: INSERM, U1099, Rennes Cedex, France, tiziano.dalbis@univ-rennes1.fr.
authors.forename: Tiziano
authors.initials: T
authors.lastname: D'Albis
authors.forename: Claire
authors.initials: C
authors.lastname: Haegelen
authors.forename: Caroline
authors.initials: C
authors.lastname: Essert
authors.forename: Sara
authors.initials: S
authors.lastname: Fernández-Vidal
authors.forename: Florent
authors.initials: F
authors.lastname: Lalys
authors.forename: Pierre
authors.initials: P
authors.lastname: Jannin
mesh_terms: D046690:Deep Brain Stimulation / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D059906:Neuroimaging / Q000379:methods; D012189:Retrospective Studies; D012984:Software; D057188:Workflow