Eric C. Frey

Junyu Chen, Eric C. Frey, Yufan He et al.

In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their substantially larger receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration.

Junyu Chen, Yufan He, Eric C. Frey et al.

In the last decade, convolutional neural networks (ConvNets) have dominated and achieved state-of-the-art performances in a variety of medical imaging applications. However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image. The recently proposed Vision Transformer (ViT) for image classification uses a purely self-attention-based model that learns long-range spatial relations to focus on the relevant parts of an image. Nevertheless, ViT emphasizes the low-resolution features because of the consecutive downsamplings, result in a lack of detailed localization information, making it unsuitable for image registration. Recently, several ViT-based image segmentation methods have been combined with ConvNets to improve the recovery of detailed localization information. Inspired by them, we present ViT-V-Net, which bridges ViT and ConvNet to provide volumetric medical image registration. The experimental results presented here demonstrate that the proposed architecture achieves superior performance to several top-performing registration methods.

Junyu Chen, Eric C. Frey

For the majority of the learning-based segmentation methods, a large quantity of high-quality training data is required. In this paper, we present a novel learning-based segmentation model that could be trained semi- or un- supervised. Specifically, in the unsupervised setting, we parameterize the Active contour without edges (ACWE) framework via a convolutional neural network (ConvNet), and optimize the parameters of the ConvNet using a self-supervised method. In another setting (semi-supervised), the auxiliary segmentation ground truth is used during training. We show that the method provides fast and high-quality bone segmentation in the context of single-photon emission computed tomography (SPECT) image.

Junyu Chen, Eric C. Frey

Pixel intensity is a widely used feature for clustering and segmentation algorithms, the resulting segmentation using only intensity values might suffer from noises and lack of spatial context information. Wavelet transform is often used for image denoising and classification. We proposed a novel method to incorporate Wavelet features in segmentation and clustering algorithms. The conventional K-means, Fuzzy c-means (FCM), and Active contour without edges (ACWE) algorithms were modified to adapt Wavelet features, leading to robust clustering/segmentation algorithms. A weighting parameter to control the weight of low-frequency sub-band information was also introduced. The new algorithms showed the capability to converge to different segmentation results based on the frequency information derived from the Wavelet sub-bands.