title: Spinal cord grey matter segmentation challenge.
abstract: An important image processing step in spinal cord magnetic resonance imaging is the ability to reliably and accurately segment grey and white matter for tissue specific analysis. There are several semi- or fully-automated segmentation methods for cervical cord cross-sectional area measurement with an excellent performance close or equal to the manual segmentation. However, grey matter segmentation is still challenging due to small cross-sectional size and shape, and active research is being conducted by several groups around the world in this field. Therefore a grey matter spinal cord segmentation challenge was organised to test different capabilities of various methods using the same multi-centre and multi-vendor dataset acquired with distinct 3D gradient-echo sequences. This challenge aimed to characterize the state-of-the-art in the field as well as identifying new opportunities for future improvements. Six different spinal cord grey matter segmentation methods developed independently by various research groups across the world and their performance were compared to manual segmentation outcomes, the present gold-standard. All algorithms provided good overall results for detecting the grey matter butterfly, albeit with variable performance in certain quality-of-segmentation metrics. The data have been made publicly available and the challenge web site remains open to new submissions. No modifications were introduced to any of the presented methods as a result of this challenge for the purposes of this publication.
authors.affiliation: 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, University College London, Russell Square, London WC1B 5EH, UK. Electronic address: f.carrasco@ucl.ac.uk.
authors.forename: Ferran
authors.initials: F
authors.lastname: Prados
authors.affiliation: Wellcome Trust Centre for Neuroimaging, University College London, Queen Square, London WC1N 3BG, UK.
authors.forename: John
authors.initials: J
authors.lastname: Ashburner
authors.affiliation: Wellcome Trust Centre for Neuroimaging, University College London, Queen Square, London WC1N 3BG, UK.
authors.forename: Claudia
authors.initials: C
authors.lastname: Blaiotta
authors.affiliation: Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Tom
authors.initials: T
authors.lastname: Brosch
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Julio
authors.initials: J
authors.lastname: Carballido-Gamio
authors.affiliation: 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, University College London, Queen Square, London WC1N 3BG, UK.
authors.forename: Manuel Jorge
authors.initials: MJ
authors.lastname: Cardoso
authors.affiliation: Department of Electrical Engineering, Computer Science, Biomedical Engineering, Radiology and Radiological Sciences, Institute of Image Science at Vanderbilt University, Nashville, TN, USA.
authors.forename: Benjamin N
authors.initials: BN
authors.lastname: Conrad
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Esha
authors.initials: E
authors.lastname: Datta
authors.affiliation: Spinal Cord Injury Center Balgrist, University Hospital Zurich, University of Zurich, Switzerland.
authors.forename: Gergely
authors.initials: G
authors.lastname: Dávid
authors.affiliation: NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, Canada.
authors.forename: Benjamin De
authors.initials: B
authors.lastname: Leener
authors.affiliation: NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, Canada.
authors.forename: Sara M
authors.initials: SM
authors.lastname: Dupont
authors.affiliation: Spinal Cord Injury Center Balgrist, University Hospital Zurich, University of Zurich, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Freund
authors.affiliation: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, University College London, Russell Square, London WC1B 5EH, UK; Brain MRI 3T Centre, C. Mondino National Neurological Institute, Pavia, Italy; Department of Brain and Behavioural Sciences, University of Pavia, Italy.
authors.forename: Claudia A M Gandini
authors.initials: CAMG
authors.lastname: Wheeler-Kingshott
authors.affiliation: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, University College London, Russell Square, London WC1B 5EH, UK.
authors.forename: Francesco
authors.initials: F
authors.lastname: Grussu
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Roland
authors.initials: R
authors.lastname: Henry
authors.affiliation: Department of Electrical Engineering, Computer Science, Biomedical Engineering, Radiology and Radiological Sciences, Institute of Image Science at Vanderbilt University, Nashville, TN, USA.
authors.forename: Bennett A
authors.initials: BA
authors.lastname: Landman
authors.affiliation: Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6T 2B5.
authors.forename: Emil
authors.initials: E
authors.lastname: Ljungberg
authors.affiliation: Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.
authors.forename: Bailey
authors.initials: B
authors.lastname: Lyttle
authors.affiliation: 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, University College London, Queen Square, London WC1N 3BG, UK.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Ourselin
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Nico
authors.initials: N
authors.lastname: Papinutto
authors.affiliation: Eindhoven University of Technology, Netherlands.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Saporito
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Regina
authors.initials: R
authors.lastname: Schlaeger
authors.affiliation: Department of Radiology and Radiological Sciences, Biomedical Engineering, Ophthalmology, Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.
authors.forename: Seth A
authors.initials: SA
authors.lastname: Smith
authors.affiliation: Department of Radiology, European Institute of Oncology, University of Modena and Reggio Emilia, 41121, Modena, MO, Italy.
authors.forename: Paul
authors.initials: P
authors.lastname: Summers
authors.affiliation: Department of Radiology, UBC MS/MRI Research Group, University of British Columbia, Vancouver, BC, Canada V6T 2B5.
authors.forename: Roger
authors.initials: R
authors.lastname: Tam
authors.affiliation: NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, University College London, Russell Square, London WC1B 5EH, UK.
authors.forename: Marios C
authors.initials: MC
authors.lastname: Yiannakas
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Alyssa
authors.initials: A
authors.lastname: Zhu
authors.affiliation: NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada. Electronic address: jcohen@polymtl.ca.
authors.forename: Julien
authors.initials: J
authors.lastname: Cohen-Adad
mesh_terms: D000328:Adult; D000465:Algorithms; D001931:Brain Mapping / Q000379:methods*; D066193:Cervical Cord / Q000033:anatomy & histology*; D005260:Female; D066128:Gray Matter / Q000033:anatomy & histology*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging; D008297:Male; D008875:Middle Aged; D015203:Reproducibility of Results; D066127:White Matter / Q000033:anatomy & histology
keywords: Challenge; Evaluation metrics; Grey matter; MRI; Segmentation; Spinal cord