SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans

Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023. The data consisted of T2-weighted MRI scans acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic, and lumbar spine. A deep learning model, SCIseg (which is open source and accessible through the Spinal Cord Toolbox, version 6.2 and above), was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg, and contrast-agnostic, all part of the Spinal Cord Toolbox). The Wilcoxon signed rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results The study included 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 [74%] male patients). SCIseg achieved a mean Dice score of 0.92 ± 0.07 and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (P = .42) and maximal axial damage ratio (P = .16) computed from manually annotated lesions and the lesion segmentations obtained using SCIseg. Conclusion SCIseg accurately segmented intramedullary lesions on a diverse dataset of T2-weighted MRI scans and automatically extracted clinically relevant lesion characteristics. Keywords: Spinal Cord, Trauma, Segmentation, MR Imaging, Supervised Learning, Convolutional Neural Network (CNN) Published under a CC BY 4.0 license.