Context. MRI of the spinal cord provides a variety of biomarkers sensitive to white matter integrity and neuronal function. Current\nprocessing methods are based on manual labeling of vertebral levels, which is time consuming and prone to user bias. Although\nseveral methods for automatic labeling have been published; they are not robust towards image contrast or towards susceptibility related\nartifacts. Methods. Intervertebral disks are detected from the 3D analysis of the intensity profile along the spine. The\nrobustness of the disk detection is improved by using a template of vertebral distance, which was generated froma training data set.\nThe developed method has been validated using T1- and T2-weighted contrasts in ten healthy subjects and one patient with spinal\ncord injury. Results. Accuracy of vertebral labeling was 100%. Mean absolute error was 2.1 �± 1.7mm for T2-weighted images and\n2.3 �± 1.6mm for T1-weighted images. The vertebrae of the spinal cord injured patient were correctly labeled, despite the presence\nof artifacts caused by metallic implants. Discussion. We proposed a template-based method for robust labeling of vertebral levels\nalong the whole spinal cord for T1- and T2-weighted contrasts. The method is freely available as part of the spinal cord toolbox.
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