David E. Newby

Simon Dahan, Hao Xu, Logan Z. J. Williams et al.

Recent state-of-the-art performances of Vision Transformers (ViT) in computer vision tasks demonstrate that a general-purpose architecture, which implements long-range self-attention, could replace the local feature learning operations of convolutional neural networks. In this paper, we extend ViTs to surfaces by reformulating the task of surface learning as a sequence-to-sequence learning problem, by proposing patching mechanisms for general surface meshes. Sequences of patches are then processed by a transformer encoder and used for classification or regression. We validate our method on a range of different biomedical surface domains and tasks: brain age prediction in the developing Human Connectome Project (dHCP), fluid intelligence prediction in the Human Connectome Project (HCP), and coronary artery calcium score classification using surfaces from the Scottish Computed Tomography of the Heart (SCOT-HEART) dataset, and investigate the impact of pretraining and data augmentation on model performance. Results suggest that Surface Vision Transformers (SiT) demonstrate consistent improvement over geometric deep learning methods for brain age and fluid intelligence prediction and achieve comparable performance on calcium score classification to standard metrics used in clinical practice. Furthermore, analysis of transformer attention maps offers clear and individualised predictions of the features driving each task. Code is available on Github: https://github.com/metrics-lab/surface-vision-transformers

Agisilaos Chartsias, Thomas Joyce, Giorgos Papanastasiou et al.

Typically, a medical image offers spatial information on the anatomy (and pathology) modulated by imaging specific characteristics. Many imaging modalities including Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) can be interpreted in this way. We can venture further and consider that a medical image naturally factors into some spatial factors depicting anatomy and factors that denote the imaging characteristics. Here, we explicitly learn this decomposed (disentangled) representation of imaging data, focusing in particular on cardiac images. We propose Spatial Decomposition Network (SDNet), which factorises 2D medical images into spatial anatomical factors and non-spatial modality factors. We demonstrate that this high-level representation is ideally suited for several medical image analysis tasks, such as semi-supervised segmentation, multi-task segmentation and regression, and image-to-image synthesis. Specifically, we show that our model can match the performance of fully supervised segmentation models, using only a fraction of the labelled images. Critically, we show that our factorised representation also benefits from supervision obtained either when we use auxiliary tasks to train the model in a multi-task setting (e.g. regressing to known cardiac indices), or when aggregating multimodal data from different sources (e.g. pooling together MRI and CT data). To explore the properties of the learned factorisation, we perform latent-space arithmetic and show that we can synthesise CT from MR and vice versa, by swapping the modality factors. We also demonstrate that the factor holding image specific information can be used to predict the input modality with high accuracy. Code will be made available at https://github.com/agis85/anatomy_modality_decomposition.

Yu Deng, Yiyang Xu, Linglong Qian et al.

Cardiac Magnetic Resonance (CMR) imaging is widely used for heart modelling and digital twin computational analysis due to its ability to visualize soft tissues and capture dynamic functions. However, the anisotropic nature of CMR images, characterized by large inter-slice distances and misalignments from cardiac motion, poses significant challenges to accurate model reconstruction. These limitations result in data loss and measurement inaccuracies, hindering the capture of detailed anatomical structures. This study introduces MorphiNet, a novel network that enhances heart model reconstruction by leveraging high-resolution Computer Tomography (CT) images, unpaired with CMR images, to learn heart anatomy. MorphiNet encodes anatomical structures as gradient fields, transforming template meshes into patient-specific geometries. A multi-layer graph subdivision network refines these geometries while maintaining dense point correspondence. The proposed method achieves high anatomy fidelity, demonstrating approximately 40% higher Dice scores, half the Hausdorff distance, and around 3 mm average surface error compared to state-of-the-art methods. MorphiNet delivers superior results with greater inference efficiency. This approach represents a significant advancement in addressing the challenges of CMR-based heart model reconstruction, potentially improving digital twin computational analyses of cardiac structure and functions.

Xiahai Zhuang, Lei Li, Christian Payer et al.

Knowledge of whole heart anatomy is a prerequisite for many clinical applications. Whole heart segmentation (WHS), which delineates substructures of the heart, can be very valuable for modeling and analysis of the anatomy and functions of the heart. However, automating this segmentation can be arduous due to the large variation of the heart shape, and different image qualities of the clinical data. To achieve this goal, a set of training data is generally needed for constructing priors or for training. In addition, it is difficult to perform comparisons between different methods, largely due to differences in the datasets and evaluation metrics used. This manuscript presents the methodologies and evaluation results for the WHS algorithms selected from the submissions to the Multi-Modality Whole Heart Segmentation (MM-WHS) challenge, in conjunction with MICCAI 2017. The challenge provides 120 three-dimensional cardiac images covering the whole heart, including 60 CT and 60 MRI volumes, all acquired in clinical environments with manual delineation. Ten algorithms for CT data and eleven algorithms for MRI data, submitted from twelve groups, have been evaluated. The results show that many of the deep learning (DL) based methods achieved high accuracy, even though the number of training datasets was limited. A number of them also reported poor results in the blinded evaluation, probably due to overfitting in their training. The conventional algorithms, mainly based on multi-atlas segmentation, demonstrated robust and stable performance, even though the accuracy is not as good as the best DL method in CT segmentation. The challenge, including the provision of the annotated training data and the blinded evaluation for submitted algorithms on the test data, continues as an ongoing benchmarking resource via its homepage (\url{www.sdspeople.fudan.edu.cn/zhuangxiahai/0/mmwhs/}).

Chengjia Wang, Gillian Macnaught, Giorgos Papanastasiou et al.

Recently, the cycle-consistent generative adversarial networks (CycleGAN) has been widely used for synthesis of multi-domain medical images. The domain-specific nonlinear deformations captured by CycleGAN make the synthesized images difficult to be used for some applications, for example, generating pseudo-CT for PET-MR attenuation correction. This paper presents a deformation-invariant CycleGAN (DicycleGAN) method using deformable convolutional layers and new cycle-consistency losses. Its robustness dealing with data that suffer from domain-specific nonlinear deformations has been evaluated through comparison experiments performed on a multi-sequence brain MR dataset and a multi-modality abdominal dataset. Our method has displayed its ability to generate synthesized data that is aligned with the source while maintaining a proper quality of signal compared to CycleGAN-generated data. The proposed model also obtained comparable performance with CycleGAN when data from the source and target domains are alignable through simple affine transformations.

Chengjia Wang, Tom MacGillivray, Gillian Macnaught et al.

Deep convolutional neural networks (CNNs) have been intensively used for multi-class segmentation of data from different modalities and achieved state-of-the-art performances. However, a common problem when dealing with large, high resolution 3D data is that the volumes input into the deep CNNs has to be either cropped or downsampled due to limited memory capacity of computing devices. These operations lead to loss of resolution and increment of class imbalance in the input data batches, which can downgrade the performances of segmentation algorithms. Inspired by the architecture of image super-resolution CNN (SRCNN) and self-normalization network (SNN), we developed a two-stage modified Unet framework that simultaneously learns to detect a ROI within the full volume and to classify voxels without losing the original resolution. Experiments on a variety of multi-modal volumes demonstrated that, when trained with a simply weighted dice coefficients and our customized learning procedure, this framework shows better segmentation performances than state-of-the-art Deep CNNs with advanced similarity metrics.

Chengjia Wang, Keith A. Goatman, James Boardman et al.

In this paper we describe improvements to the particle swarm optimizer (PSO) made by inclusion of an unscented Kalman filter to guide particle motion. We demonstrate the effectiveness of the unscented Kalman filter PSO by comparing it with the original PSO algorithm and its variants designed to improve performance. The PSOs were tested firstly on a number of common synthetic benchmarking functions, and secondly applied to a practical three-dimensional image registration problem. The proposed methods displayed better performances for 4 out of 8 benchmark functions, and reduced the target registration errors by at least 2mm when registering down-sampled benchmark brain images. Our methods also demonstrated an ability to align images featuring motion related artefacts which all other methods failed to register. These new PSO methods provide a novel, efficient mechanism to integrate prior knowledge into each iteration of the optimization process, which can enhance the accuracy and speed of convergence in the application of medical image registration.