Brain tumor segmentation using 3D Mask R-CNN for dynamic susceptibility contrast enhanced perfusion imaging

The segmentation of neoplasms is an important part of radiotherapy treatment planning, monitoring disease progression, and predicting patient outcome. In the brain, functional magnetic resonance imaging (MRI) like dynamic susceptibility contrast enhanced (DSCE) or T1-weighted dynamic contrast enhanced (DCE) perfusion MRI are important tools for diagnosis. They play a crucial role in providing pre-operative assessment of tumor histology, grading, and biopsy guidance. However, the manual contouring of these neoplasms is tedious, expensive, time-consuming, and vulnerable to inter-observer variability. In this work, we propose a 3D mask region-based convolutional neural network (R-CNN) method to automatically segment brain tumors in DSCE MRI perfusion images. As our goal is to simultaneously localize and segment the tumor, our training process contained both a region-of-interest (ROI) localization and regression with voxel-wise segmentation. The combination of classification loss, ROI location and size regression loss, and segmentation loss were used to supervise the proposed network. We retrospectively investigated 21 patients' perfusion images, with between 50 and 70 perfusion time point volumes, a total of 1260 3D volumes. Tumor contours were automatically segmented by our proposed method and compared against other state-of-the-art methods and those delineated by physicians as the ground truth. The results of our method demonstrated good agreement with the ground truth contours. The average DSC, precision, recall, Hausdorff distance, mean surface distance (MSD), root MSD, and center of mass distance were 0.90 +/- 0.04, 0.91 +/- 0.04, 0.90 +/- 0.06, 7.16 +/- 5.78 mm, 0.45 +/- 0.34 mm, 1.03 +/- 0.72 mm, and 0.86 +/- 0.91 mm, respectively. These results support the feasibility of our method in accurately localizing and segmenting brain tumors in DSCE perfusion MRI. Our 3D Mask R-CNN segmentation method in DSCE perfusion imaging has great promise for future clinical use.