title: Fast and accurate semi-automated segmentation method of spinal cord MR images at 3T applied to the construction of a cervical spinal cord template.
abstract: OBJECTIVE
  To design a fast and accurate semi-automated segmentation method for spinal cord 3T MR images and to construct a template of the cervical spinal cord.
  
  
  METHODS
  A semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was also quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects' images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map.
  
  
  RESULTS
  Visual scoring showed better performance for DTbM than for ASM. Mean Dice similarity coefficient (DSC) was 95.71% for DTbM and 90.78% for ASM at the cervical level and 94.27% for DTbM and 89.93% for ASM at the thoracic level. Finally, at C2 vertebral level, mean DSC was 97.98% for DTbM compared with 98.02% for TbM and 96.76% for ASM. DTbM showed similar accuracy compared with TbM, but with the advantage of limited manual interaction.
  
  
  CONCLUSIONS
  A semi-automated segmentation method with limited manual intervention was introduced and validated on 3T images, enabling the construction of a cervical spinal cord template.
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Mohamed-Mounir
authors: MM
authors: El Mendili
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Raphaël
authors: R
authors: Chen
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Brice
authors: B
authors: Tiret
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Noémie
authors: N
authors: Villard
authors: APHP, Groupe Hospitalier Pitié-Salpêtrière, Service de Neuroradiologie, F-75013, Paris, Île de France, France.
authors: Stéphanie
authors: S
authors: Trunet
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Mélanie
authors: M
authors: Pélégrini-Issac
authors: APHP, Groupe Hospitalier Pitié-Salpêtrière, Service de Neuroradiologie, F-75013, Paris, Île de France, France; Sorbonne Universités, UPMC Univ Paris 06, UMR-S975, Inserm U975, CNRS UMR7225, Centre de recherche de l'Institut du Cerveau et de la Moelle épinière-CRICM, Centre de Neuroimagerie de Recherche-CENIR, F-75013, Paris, Île de France, France.
authors: Stéphane
authors: S
authors: Lehéricy
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Département des Maladies du Système Nerveux, F-75013, Paris, Île de France, France.
authors: Pierre-François
authors: PF
authors: Pradat
authors: Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75013, Paris, Île de France, France.
authors: Habib
authors: H
authors: Benali
mesh_terms: D000690:Amyotrophic Lateral Sclerosis / Q000000981:diagnostic imaging; D001331:Automation; D066193:Cervical Cord / Q000000981:diagnostic imaging*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009134:Muscular Atrophy, Spinal / Q000000981:diagnostic imaging; D011859:Radiography; D013119:Spinal Cord Injuries / Q000000981:diagnostic imaging