论文标题
深度学习的MRI上的多类脊髓肿瘤分割
Multiclass Spinal Cord Tumor Segmentation on MRI with Deep Learning
论文作者
论文摘要
脊髓肿瘤导致神经系统发病和死亡率。能够获得肿瘤,水肿和空腔的形态定量(大小,位置,生长速率)可以改善监测和治疗计划。这种定量要求将这些结构分割成三个单独的类。但是,三维结构的手动分割是耗时且乏味的,激发了自动化方法的发展。在这里,我们量身定制适合脊髓肿瘤分割任务的模型。使用宫颈,胸腔和/或腰部覆盖率的T2加权和T2加权MRI扫描从343例患者那里获得了343例患者。该数据集包括三种最常见的髓内脊髓肿瘤类型:星形胶质细胞瘤,室膜膜瘤和血管母细胞瘤。所提出的方法是一种级联的架构,具有基于U-NET的模型,该模型将肿瘤分为两个阶段的过程:定位和标签。该模型首先找到脊髓并生成边界盒坐标。图像是根据此输出裁剪的,导致视野降低,从而减轻了类失衡。然后分割肿瘤。肿瘤,腔和水肿的细分(单个类)达到76.7 $ \ pm的骰子分数$ 1.5%,仅肿瘤的分割达到61.8 $ \ pm $ 4.0%$ 4.0%。对于肿瘤,水肿和腔体的真正阳性检测率高于87%。据我们所知,这是第一个用于脊髓肿瘤分割的全自动深学习模型。多类分割管道可在脊髓工具箱(https://spinalcordtoolbox.com/)中获得。它可以在几秒钟内使用普通计算机上的自定义数据运行。
Spinal cord tumors lead to neurological morbidity and mortality. Being able to obtain morphometric quantification (size, location, growth rate) of the tumor, edema, and cavity can result in improved monitoring and treatment planning. Such quantification requires the segmentation of these structures into three separate classes. However, manual segmentation of 3-dimensional structures is time-consuming and tedious, motivating the development of automated methods. Here, we tailor a model adapted to the spinal cord tumor segmentation task. Data were obtained from 343 patients using gadolinium-enhanced T1-weighted and T2-weighted MRI scans with cervical, thoracic, and/or lumbar coverage. The dataset includes the three most common intramedullary spinal cord tumor types: astrocytomas, ependymomas, and hemangioblastomas. The proposed approach is a cascaded architecture with U-Net-based models that segments tumors in a two-stage process: locate and label. The model first finds the spinal cord and generates bounding box coordinates. The images are cropped according to this output, leading to a reduced field of view, which mitigates class imbalance. The tumor is then segmented. The segmentation of the tumor, cavity, and edema (as a single class) reached 76.7 $\pm$ 1.5% of Dice score and the segmentation of tumors alone reached 61.8 $\pm$ 4.0% Dice score. The true positive detection rate was above 87% for tumor, edema, and cavity. To the best of our knowledge, this is the first fully automatic deep learning model for spinal cord tumor segmentation. The multiclass segmentation pipeline is available in the Spinal Cord Toolbox (https://spinalcordtoolbox.com/). It can be run with custom data on a regular computer within seconds.