Multimodal MRI brain tumor segmentation using random forests with features learned from fully convolutional neural network

In this paper, we propose a novel learning based method for automated segmentation of brain tumor in multimodal MRI images. The machine learned features from fully convolutional neural network (FCN) and hand-designed texton features are used to classify the MRI image voxels. The score map with pixelwise predictions is used as a feature map which is learned from multimodal MRI training dataset using the FCN. The learned features are then applied to random forests to classify each MRI image voxel into normal brain tissues and different parts of tumor. The method was evaluated on BRATS 2013 challenge dataset. The results show that the application of the random forest classifier to multimodal MRI images using machine-learned features based on FCN and hand-designed features based on textons provides promising segmentations. The Dice overlap measure for automatic brain tumor segmentation against ground truth is 0.88, 080 and 0.73 for complete tumor, core and enhancing tumor, respectively.