Osteoporotic and Neoplastic Compression Fracture Classification on Longitudinal CT

Classification of vertebral compression fractures (VCF) having osteoporotic or neoplastic origin is fundamental to the planning of treatment. We developed a fracture classification system by acquiring quantitative morphologic and bone density determinants of fracture progression through the use of automated measurements from longitudinal studies. A total of 250 CT studies were acquired for the task, each having previously identified VCFs with osteoporosis or neoplasm. Thirty-six features or each identified VCF were computed and classified using a committee of support vector machines. Ten-fold cross validation on 695 identified fractured vertebrae showed classification accuracies of 0.812, 0.665, and 0.820 for the measured, longitudinal, and combined feature sets respectively.Comment: Contributed 4-Page Paper to be presented at the 2016 IEEE International Symposium on Biomedical Imaging (ISBI), April 13-16, 2016, Prague, Czech Republi

RAR-U-Net: a Residual Encoder to Attention Decoder by Residual Connections Framework for Spine Segmentation under Noisy Labels

Segmentation algorithms of medical image volumes are widely studied for many clinical and research purposes. We propose a novel and efficient framework for medical image segmentation. The framework functions under a deep learning paradigm, incorporating four novel contributions. Firstly, a residual interconnection is explored in different scale encoders. Secondly, four copy and crop connections are replaced to residual-block-based concatenation to alleviate the disparity between encoders and decoders, respectively. Thirdly, convolutional attention modules for feature refinement are studied on all scale decoders. Finally, an adaptive denoising learning strategy(ADL) based on the training process from underfitting to overfitting is studied. Experimental results are illustrated on a publicly available benchmark database of spine CTs. Our segmentation framework achieves competitive performance with other state-of-the-art methods over a variety of different evaluation measures

Comparing Normalization Methods for Limited Batch Size Segmentation Neural Networks

The widespread use of Batch Normalization has enabled training deeper neural networks with more stable and faster results. However, the Batch Normalization works best using large batch size during training and as the state-of-the-art segmentation convolutional neural network architectures are very memory demanding, large batch size is often impossible to achieve on current hardware. We evaluate the alternative normalization methods proposed to solve this issue on a problem of binary spine segmentation from 3D CT scan. Our results show the effectiveness of Instance Normalization in the limited batch size neural network training environment. Out of all the compared methods the Instance Normalization achieved the highest result with Dice coefficient = 0.96 which is comparable to our previous results achieved by deeper network with longer training time. We also show that the Instance Normalization implementation used in this experiment is computational time efficient when compared to the network without any normalization method

Dealing with unreliable annotations: noise-robust network for semantic segmentation through transformer-improved-encoder and convolution-decoder

Conventional deep learning methods have shown promising results in the medical domain when trained on accurate ground truth data. Pragmatically, due to constraints like lack of time or annotator inexperience, the ground truth data obtained from clinical environments may not always be impeccably accurate. In this paper, we investigate whether the presence of noise in ground truth data can be mitigated. We propose an innovative and efficient approach that addresses the challenge posed by noise in segmentation labels. Our method consists of four key components within a deep learning framework. First, we introduce a Vision Transformer-based modified encoder combined with a convolution-based decoder for the segmentation network, capitalizing on the recent success of self-attention mechanisms. Second, we consider a public CT spine segmentation dataset and devise a preprocessing step to generate (and even exaggerate) noisy labels, simulating real-world clinical situations. Third, to counteract the influence of noisy labels, we incorporate an adaptive denoising learning strategy (ADL) into the network training. Finally, we demonstrate through experimental results that the proposed method achieves noise-robust performance, outperforming existing baseline segmentation methods across multiple evaluation metrics