title: Spinal Cord Segmentation by One Dimensional Normalized Template Matching: A Novel, Quantitative Technique to Analyze Advanced Magnetic Resonance Imaging Data.
abstract: Spinal cord segmentation is a developing area of research intended to aid the processing and interpretation of advanced magnetic resonance imaging (MRI). For example, high resolution three-dimensional volumes can be segmented to provide a measurement of spinal cord atrophy. Spinal cord segmentation is difficult due to the variety of MRI contrasts and the variation in human anatomy. In this study we propose a new method of spinal cord segmentation based on one-dimensional template matching and provide several metrics that can be used to compare with other segmentation methods. A set of ground-truth data from 10 subjects was manually-segmented by two different raters. These ground truth data formed the basis of the segmentation algorithm. A user was required to manually initialize the spinal cord center-line on new images, taking less than one minute. Template matching was used to segment the new cord and a refined center line was calculated based on multiple centroids within the segmentation. Arc distances down the spinal cord and cross-sectional areas were calculated. Inter-rater validation was performed by comparing two manual raters (n = 10). Semi-automatic validation was performed by comparing the two manual raters to the semi-automatic method (n = 10). Comparing the semi-automatic method to one of the raters yielded a Dice coefficient of 0.91 +/- 0.02 for ten subjects, a mean distance between spinal cord center lines of 0.32 +/- 0.08 mm, and a Hausdorff distance of 1.82 +/- 0.33 mm. The absolute variation in cross-sectional area was comparable for the semi-automatic method versus manual segmentation when compared to inter-rater manual segmentation. The results demonstrate that this novel segmentation method performs as well as a manual rater for most segmentation metrics. It offers a new approach to study spinal cord disease and to quantitatively track changes within the spinal cord in an individual case and across cohorts of subjects.
authors.affiliation: Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Adam
authors.initials: A
authors.lastname: Cadotte
authors.affiliation: Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada; Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada.
authors.forename: David W
authors.initials: DW
authors.lastname: Cadotte
authors.affiliation: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Micha
authors.initials: M
authors.lastname: Livne
authors.affiliation: Institute of Biomedical Engineering, Ecole Polytechnique de Montréal, Montreal, Quebec, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, Quebec, Canada.
authors.forename: Julien
authors.initials: J
authors.lastname: Cohen-Adad
authors.affiliation: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Fleet
authors.affiliation: Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada; Department of Medical Imaging, Division of Neuroradiology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Mikulis
authors.affiliation: Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada; Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada; University of Toronto Spine Program, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Fehlings
mesh_terms: D000328:Adult; D000465:Algorithms; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008875:Middle Aged; D013116:Spinal Cord / Q000033:anatomy & histology* / Q000473:pathology / Q000648:ultrastructure*; D055815:Young Adult