title: Fully automated grey and white matter spinal cord segmentation.
abstract: Axonal loss in the spinal cord is one of the main contributing factors to irreversible clinical disability in multiple sclerosis (MS). In vivo axonal loss can be assessed indirectly by estimating a reduction in the cervical cross-sectional area (CSA) of the spinal cord over time, which is indicative of spinal cord atrophy, and such a measure may be obtained by means of image segmentation using magnetic resonance imaging (MRI). In this work, we propose a new fully automated spinal cord segmentation technique that incorporates two different multi-atlas segmentation propagation and fusion techniques: The Optimized PatchMatch Label fusion (OPAL) algorithm for localising and approximately segmenting the spinal cord, and the Similarity and Truth Estimation for Propagated Segmentations (STEPS) algorithm for segmenting white and grey matter simultaneously. In a retrospective analysis of MRI data, the proposed method facilitated CSA measurements with accuracy equivalent to the inter-rater variability, with a Dice score (DSC) of 0.967 at C2/C3 level. The segmentation performance for grey matter at C2/C3 level was close to inter-rater variability, reaching an accuracy (DSC) of 0.826 for healthy subjects and 0.835 people with clinically isolated syndrome MS.
authors: Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK.|NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Ferran
authors: F
authors: Prados
authors: Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK.|Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
authors: M Jorge
authors: MJ
authors: Cardoso
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Marios C
authors: MC
authors: Yiannakas
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Luke R
authors: LR
authors: Hoy
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Elisa
authors: E
authors: Tebaldi
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Hugh
authors: H
authors: Kearney
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Martina D
authors: MD
authors: Liechti
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: David H
authors: DH
authors: Miller
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.
authors: Olga
authors: O
authors: Ciccarelli
authors: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, 1st Floor, Russell Square House, 10-12 Russell Square, London, WC1B 5EH, UK.|Brain MRI 3T Center, C. Mondino National Neurological Institute, Pavia, Italy.
authors: Claudia A M Gandini
authors: CA
authors: Wheeler-Kingshott
authors: Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK.|Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
authors: Sebastien
authors: S
authors: Ourselin
mesh_terms: D000328:Adult; D000465:Algorithms; D001331:Automation; D005260:Female; D066128:Gray Matter / Q000000981:diagnostic imaging; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging; D008297:Male; D008875:Middle Aged; D009103:Multiple Sclerosis / Q000473:pathology; D013116:Spinal Cord / Q000000981:diagnostic imaging*; D066127:White Matter / Q000000981:diagnostic imaging