Cardiac magnetic resonance (CMR) is a key investigation in clinical cardiovascular medicine and has been used extensively in population research. However, extracting clinically important measurements such as ejection fraction for diagnosing cardiovascular diseases remains time-consuming and subjective. We developed CineMA, a foundation AI model automating these tasks with limited labels. CineMA is a self-supervised autoencoder model trained on 74,916 cine CMR studies to reconstruct images from masked inputs. After fine-tuning, it was evaluated across eight datasets on 23 tasks from four categories: ventricle and myocardium segmentation, left and right ventricle ejection fraction calculation, disease detection and classification, and landmark localisation. CineMA is the first foundation model for cine CMR to match or outperform convolutional neural networks (CNNs). CineMA demonstrated greater label efficiency than CNNs, achieving comparable or better performance with fewer annotations. This reduces the burden of clinician labelling and supports replacing task-specific training with fine-tuning foundation models in future cardiac imaging applications. Models and code for pre-training and fine-tuning are available at https://github.com/mathpluscode/CineMA, democratising access to high-performance models that otherwise require substantial computational resources, promoting reproducibility and accelerating clinical translation.
Cardiac T1 mapping can evaluate various clinical symptoms of myocardial tissue. However, there is currently a lack of effective, robust, and efficient methods for motion correction in cardiac T1 mapping. In this paper, we propose a deep learning-based and topology-preserving image registration framework for motion correction in cardiac T1 mapping. Notably, our proposed implicit consistency constraint dubbed BLOC, to some extent preserves the image topology in registration by bidirectional consistency constraint and local anti-folding constraint. To address the contrast variation issue, we introduce a weighted image similarity metric for multimodal registration of cardiac T1-weighted images. Besides, a semi-supervised myocardium segmentation network and a dual-domain attention module are integrated into the framework to further improve the performance of the registration. Numerous comparative experiments, as well as ablation studies, demonstrated the effectiveness and high robustness of our method. The results also indicate that the proposed weighted image similarity metric, specifically crafted for our network, contributes a lot to the enhancement of the motion correction efficacy, while the bidirectional consistency constraint combined with the local anti-folding constraint ensures a more desirable topology-preserving registration mapping.
Left ventricular ejection fraction (LVEF) is the most important clinical parameter of cardiovascular function. The accuracy in estimating this parameter is highly dependent upon the precise segmentation of the left ventricle (LV) structure at the end diastole and systole phases. Therefore, it is crucial to develop robust algorithms for the precise segmentation of the heart structure during different phases. Methodology: In this work, an improved 3D UNet model is introduced to segment the myocardium and LV, while excluding papillary muscles, as per the recommendation of the Society for Cardiovascular Magnetic Resonance. For the practical testing of the proposed framework, a total of 8,400 cardiac MRI images were collected and analysed from the military hospital in Tunis (HMPIT), as well as the popular ACDC public dataset. As performance metrics, we used the Dice coefficient and the F1 score for validation/testing of the LV and the myocardium segmentation. Results: The data was split into 70%, 10%, and 20% for training, validation, and testing, respectively. It is worth noting that the proposed segmentation model was tested across three axis views: basal, medio basal and apical at two different cardiac phases: end diastole and end systole instances. The experimental results showed a Dice index of 0.965 and 0.945, and an F1 score of 0.801 and 0.799, at the end diastolic and systolic phases, respectively. Additionally, clinical evaluation outcomes revealed a significant difference in the LVEF and other clinical parameters when the papillary muscles were included or excluded.
This study provides a comparative analysis of deep learning models including UNet, Res-UNet, Attention Res-UNet, and nnUNet, and evaluates their performance in brain tumour, polyp, and multi-class heart segmentation tasks. The analysis focuses on precision, accuracy, recall, Dice Similarity Coefficient (DSC), and Intersection over Union (IoU) to assess their clinical applicability. In brain tumour segmentation, Res-UNet and nnUNet significantly outperformed UNet, with Res-UNet leading in DSC and IoU scores, indicating superior accuracy in tumour delineation. Meanwhile, nnUNet excelled in recall and accuracy, which are crucial for reliable tumour detection in clinical diagnosis and planning. In polyp detection, nnUNet was the most effective, achieving the highest metrics across all categories and proving itself as a reliable diagnostic tool in endoscopy. In the complex task of heart segmentation, Res-UNet and Attention Res-UNet were outstanding in delineating the left ventricle, with Res-UNet also leading in right ventricle segmentation. nnUNet was unmatched in myocardium segmentation, achieving top scores in precision, recall, DSC, and IoU. The conclusion notes that although Res-UNet occasionally outperforms nnUNet in specific metrics, the differences are quite small. Moreover, nnUNet consistently shows superior overall performance across the experiments. Particularly noted for its high recall and accuracy, which are crucial in clinical settings to minimize misdiagnosis and ensure timely treatment, nnUNet's robust performance in crucial metrics across all tested categories establishes it as the most effective model for these varied and complex segmentation tasks.
In cardiac Magnetic Resonance Imaging (MRI) analysis, simultaneous myocardial segmentation and T2 quantification are crucial for assessing myocardial pathologies. Existing methods often address these tasks separately, limiting their synergistic potential. To address this, we propose SQNet, a dual-task network integrating Transformer and Convolutional Neural Network (CNN) components. SQNet features a T2-refine fusion decoder for quantitative analysis, leveraging global features from the Transformer, and a segmentation decoder with multiple local region supervision for enhanced accuracy. A tight coupling module aligns and fuses CNN and Transformer branch features, enabling SQNet to focus on myocardium regions. Evaluation on healthy controls (HC) and acute myocardial infarction patients (AMI) demonstrates superior segmentation dice scores (89.3/89.2) compared to state-of-the-art methods (87.7/87.9). T2 quantification yields strong linear correlations (Pearson coefficients: 0.84/0.93) with label values for HC/AMI, indicating accurate mapping. Radiologist evaluations confirm SQNet's superior image quality scores (4.60/4.58 for segmentation, 4.32/4.42 for T2 quantification) over state-of-the-art methods (4.50/4.44 for segmentation, 3.59/4.37 for T2 quantification). SQNet thus offers accurate simultaneous segmentation and quantification, enhancing cardiac disease diagnosis, such as AMI.
Accurate myocardium segmentation across all phases in one cardiac cycle in cine cardiac magnetic resonance (CMR) scans is crucial for comprehensively cardiac function analysis. Despite advancements in deep learning (DL) for automatic cine CMR segmentation, generalizability on unseen data remains a significant challenge. Recently, the segment-anything-model (SAM) has been invented as a segmentation foundation model, known for its accurate segmentation and more importantly, zero-shot generalization. SAM was trained on two-dimensional (2D) natural images; to adapt it for comprehensive cine CMR segmentation, we propose cineCMR-SAM which incorporates both temporal and spatial information through a modified model architecture. Compared to other state-of-the-art (SOTA) methods, our model achieved superior data-specific model segmentation accuracy on the STACOM2011 when fine-tuned on this dataset and demonstrated superior zero-shot generalization on two other large public datasets (ACDC and M&Ms) unseen during fine-tuning. Additionally, we introduced a text prompt feature in cineCMR-SAM to specify the view type of input slices (short-axis or long-axis), enhancing performance across all view types.
The presence of domain shift in medical imaging is a common issue, which can greatly impact the performance of segmentation models when dealing with unseen image domains. Adversarial-based deep learning models, such as Cycle-GAN, have become a common model for approaching unsupervised domain adaptation of medical images. These models however, have no ability to enforce the preservation of structures of interest when translating medical scans, which can lead to potentially poor results for unsupervised domain adaptation within the context of segmentation. This work introduces the Structure Preserving Cycle-GAN (SP Cycle-GAN), which promotes medical structure preservation during image translation through the enforcement of a segmentation loss term in the overall Cycle-GAN training process. We demonstrate the structure preserving capability of the SP Cycle-GAN both visually and through comparison of Dice score segmentation performance for the unsupervised domain adaptation models. The SP Cycle-GAN is able to outperform baseline approaches and standard Cycle-GAN domain adaptation for binary blood vessel segmentation in the STARE and DRIVE datasets, and multi-class Left Ventricle and Myocardium segmentation in the multi-modal MM-WHS dataset. SP Cycle-GAN achieved a state of the art Myocardium segmentation Dice score (DSC) of 0.7435 for the MR to CT MM-WHS domain adaptation problem, and excelled in nearly all categories for the MM-WHS dataset. SP Cycle-GAN also demonstrated a strong ability to preserve blood vessel structure in the DRIVE to STARE domain adaptation problem, achieving a 4% DSC increase over a default Cycle-GAN implementation.
Automated identification of myocardial scar from late gadolinium enhancement cardiac magnetic resonance images (LGE-CMR) is limited by image noise and artifacts such as those related to motion and partial volume effect. This paper presents a novel joint deep learning (JDL) framework that improves such tasks by utilizing simultaneously learned myocardium segmentations to eliminate negative effects from non-region-of-interest areas. In contrast to previous approaches treating scar detection and myocardium segmentation as separate or parallel tasks, our proposed method introduces a message passing module where the information of myocardium segmentation is directly passed to guide scar detectors. This newly designed network will efficiently exploit joint information from the two related tasks and use all available sources of myocardium segmentation to benefit scar identification. We demonstrate the effectiveness of JDL on LGE-CMR images for automated left ventricular (LV) scar detection, with great potential to improve risk prediction in patients with both ischemic and non-ischemic heart disease and to improve response rates to cardiac resynchronization therapy (CRT) for heart failure patients. Experimental results show that our proposed approach outperforms multiple state-of-the-art methods, including commonly used two-step segmentation-classification networks, and multitask learning schemes where subtasks are indirectly interacted.
Accurate segmentation and motion estimation of myocardium have always been important in clinic field, which essentially contribute to the downstream diagnosis. However, existing methods cannot always guarantee the shape integrity for myocardium segmentation. In addition, motion estimation requires point correspondence on the myocardium region across different frames. In this paper, we propose a novel end-to-end deep statistic shape model to focus on myocardium segmentation with both shape integrity and boundary correspondence preserving. Specifically, myocardium shapes are represented by a fixed number of points, whose variations are extracted by Principal Component Analysis (PCA). Deep neural network is used to predict the transformation parameters (both affine and deformation), which are then used to warp the mean point cloud to the image domain. Furthermore, a differentiable rendering layer is introduced to incorporate mask supervision into the framework to learn more accurate point clouds. In this way, the proposed method is able to consistently produce anatomically reasonable segmentation mask without post processing. Additionally, the predicted point cloud guarantees boundary correspondence for sequential images, which contributes to the downstream tasks, such as the motion estimation of myocardium. We conduct several experiments to demonstrate the effectiveness of the proposed method on several benchmark datasets.
Temporal patterns of cardiac motion provide important information for cardiac disease diagnosis. This pattern could be obtained by three-directional CINE multi-slice left ventricular myocardial velocity mapping (3Dir MVM), which is a cardiac MR technique providing magnitude and phase information of the myocardial motion simultaneously. However, long acquisition time limits the usage of this technique by causing breathing artifacts, while shortening the time causes low temporal resolution and may provide an inaccurate assessment of cardiac motion. In this study, we proposed a frame synthesis algorithm to increase the temporal resolution of 3Dir MVM data. Our algorithm is featured by 1) three attention-based encoders which accept magnitude images, phase images, and myocardium segmentation masks respectively as inputs; 2) three decoders that output the interpolated frames and corresponding myocardium segmentation results; and 3) loss functions highlighting myocardium pixels. Our algorithm can not only increase the temporal resolution 3Dir MVMs, but can also generates the myocardium segmentation results at the same time.
Accurate topology is key when performing meaningful anatomical segmentations, however, it is often overlooked in traditional deep learning methods. In this work we propose TEDS-Net: a novel segmentation method that guarantees accurate topology. Our method is built upon a continuous diffeomorphic framework, which enforces topology preservation. However, in practice, diffeomorphic fields are represented using a finite number of parameters and sampled using methods such as linear interpolation, violating the theoretical guarantees. We therefore introduce additional modifications to more strictly enforce it. Our network learns how to warp a binary prior, with the desired topological characteristics, to complete the segmentation task. We tested our method on myocardium segmentation from an open-source 2D heart dataset. TEDS-Net preserved topology in 100% of the cases, compared to 90% from the U-Net, without sacrificing on Hausdorff Distance or Dice performance. Code will be made available at: www.github.com/mwyburd/TEDS-Net
In this work, the best size for late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) images in the training dataset was determined to optimize deep learning training outcomes. Non-extra pixel and extra pixel interpolation algorithms were used to determine the new size of the LGE-MRI images. A novel strategy was introduced to handle interpolation masks and remove extra class labels in interpolated ground truth (GT) segmentation masks. The expectation maximization, weighted intensity, a priori information (EWA) algorithm was used for quantification of myocardial infarction (MI) in automatically segmented LGE-MRI images. Arbitrary threshold, comparison of the sums, and sums of differences are methods used to estimate the relationship between semi-automatic or manual and fully automated quantification of myocardial infarction (MI) results. The relationship between semi-automatic and fully automated quantification of MI results was found to be closer in the case of bigger LGE MRI images (55.5% closer to manual results) than in the case of smaller LGE MRI images (22.2% closer to manual results).
Visualizing disease-induced scarring and fibrosis in the heart on cardiac magnetic resonance (CMR) imaging with contrast enhancement (LGE) is paramount in characterizing disease progression and quantifying pathophysiological substrates of arrhythmias. However, segmentation and scar/fibrosis identification from LGE-CMR is an intensive manual process prone to large inter-observer variability. Here, we present a novel fully-automated anatomically-informed deep learning solution for left ventricle (LV) and scar/fibrosis segmentation and clinical feature extraction from LGE-CMR. The technology involves three cascading convolutional neural networks that segment myocardium and scar/fibrosis from raw LGE-CMR images and constrain these segmentations within anatomical guidelines, thus facilitating seamless derivation of clinically-significant parameters. In addition to available LGE-CMR images, training used "LGE-like" synthetically enhanced cine scans. Results show excellent agreement with those of trained experts in terms of segmentation (balanced accuracy of $96\%$ and $75\%$ for LV and scar segmentation), clinical features ($2\%$ difference in mean scar-to-LV wall volume fraction), and anatomical fidelity. Our segmentation technology is extendable to other computer vision medical applications and to problems requiring guidelines adherence of predicted outputs.
Segmentation of anatomical regions of interest such as vessels or small lesions in medical images is still a difficult problem that is often tackled with manual input by an expert. One of the major challenges for this task is that the appearance of foreground (positive) regions can be similar to background (negative) regions. As a result, many automatic segmentation algorithms tend to exhibit asymmetric errors, typically producing more false positives than false negatives. In this paper, we aim to leverage this asymmetry and train a diverse ensemble of models with very high recall, while sacrificing their precision. Our core idea is straightforward: A diverse ensemble of low precision and high recall models are likely to make different false positive errors (classifying background as foreground in different parts of the image), but the true positives will tend to be consistent. Thus, in aggregate the false positive errors will cancel out, yielding high performance for the ensemble. Our strategy is general and can be applied with any segmentation model. In three different applications (carotid artery segmentation in a neck CT angiography, myocardium segmentation in a cardiovascular MRI and multiple sclerosis lesion segmentation in a brain MRI), we show how the proposed approach can significantly boost the performance of a baseline segmentation method.
Current deep-learning-based registration algorithms often exploit intensity-based similarity measures as the loss function, where dense correspondence between a pair of moving and fixed images is optimized through backpropagation during training. However, intensity-based metrics can be misleading when the assumption of intensity class correspondence is violated, especially in cross-modality or contrast-enhanced images. Moreover, existing learning-based registration methods are predominantly applicable to pairwise registration and are rarely extended to groupwise registration or simultaneous registration with multiple images. In this paper, we propose a new image registration framework based on multivariate mixture model (MvMM) and neural network estimation. A generative model consolidating both appearance and anatomical information is established to derive a novel loss function capable of implementing groupwise registration. We highlight the versatility of the proposed framework for various applications on multimodal cardiac images, including single-atlas-based segmentation (SAS) via pairwise registration and multi-atlas segmentation (MAS) unified by groupwise registration. We evaluated performance on two publicly available datasets, i.e. MM-WHS-2017 and MS-CMRSeg-2019. The results show that the proposed framework achieved an average Dice score of $0.871\pm 0.025$ for whole-heart segmentation on MR images and $0.783\pm 0.082$ for myocardium segmentation on LGE MR images.
With the advent of Cardiac Cine Magnetic Resonance (CMR) Imaging, there has been a paradigm shift in medical technology, thanks to its capability of imaging different structures within the heart without ionizing radiation. However, it is very challenging to conduct pre-operative planning of minimally invasive cardiac procedures without accurate segmentation and identification of the left ventricle (LV), right ventricle (RV) blood-pool, and LV-myocardium. Manual segmentation of those structures, nevertheless, is time-consuming and often prone to error and biased outcomes. Hence, automatic and computationally efficient segmentation techniques are paramount. In this work, we propose a novel memory-efficient Convolutional Neural Network (CNN) architecture as a modification of both CondenseNet, as well as DenseNet for ventricular blood-pool segmentation by introducing a bottleneck block and an upsampling path. Our experiments show that the proposed architecture runs on the Automated Cardiac Diagnosis Challenge (ACDC) dataset using half (50%) the memory requirement of DenseNet and one-twelfth (~ 8%) of the memory requirements of U-Net, while still maintaining excellent accuracy of cardiac segmentation. We validated the framework on the ACDC dataset featuring one healthy and four pathology groups whose heart images were acquired throughout the cardiac cycle and achieved the mean dice scores of 96.78% (LV blood-pool), 93.46% (RV blood-pool) and 90.1% (LV-Myocardium). These results are promising and promote the proposed methods as a competitive tool for cardiac image segmentation and clinical parameter estimation that has the potential to provide fast and accurate results, as needed for pre-procedural planning and/or pre-operative applications.
Myocardium segmentation of late gadolinium enhancement (LGE) Cardiac MR images is important for evaluation of infarction regions in clinical practice. The pathological myocardium in LGE images presents distinctive brightness and textures compared with the healthy tissues, making it much more challenging to be segment. Instead, the balanced-Steady State Free Precession (bSSFP) cine images show clearly boundaries and can be easily segmented. Given this fact, we propose a novel shape-transfer GAN for LGE images, which can 1) learn to generate realistic LGE images from bSSFP with the anatomical shape preserved, and 2) learn to segment the myocardium of LGE images from these generated images. It's worth to note that no segmentation label of the LGE images is used during this procedure. We test our model on dataset from the Multi-sequence Cardiac MR Segmentation Challenge. The results show that the proposed Shape-Transfer GAN can achieve accurate myocardium masks of LGE images.
Accurate segmentation of the left ventricle myocardium in cardiac CT angiography (CCTA) is essential for e.g. the assessment of myocardial perfusion. Automatic deep learning methods for segmentation in CCTA might suffer from differences in contrast-agent attenuation between training and test data due to non-standardized contrast administration protocols and varying cardiac output. We propose augmentation of the training data with virtual mono-energetic reconstructions from a spectral CT scanner which show different attenuation levels of the contrast agent. We compare this to an augmentation by linear scaling of all intensity values, and combine both types of augmentation. We train a 3D fully convolutional network (FCN) with 10 conventional CCTA images and corresponding virtual mono-energetic reconstructions acquired on a spectral CT scanner, and evaluate on 40 CCTA scans acquired on a conventional CT scanner. We show that training with data augmentation using virtual mono-energetic images improves upon training with only conventional images (Dice similarity coefficient (DSC) 0.895 $\pm$ 0.039 vs. 0.846 $\pm$ 0.125). In comparison, training with data augmentation using linear scaling improves the DSC to 0.890 $\pm$ 0.039. Moreover, combining the results of both augmentation methods leads to a DSC of 0.901 $\pm$ 0.036, showing that both augmentations lead to different local improvements of the segmentations. Our results indicate that virtual mono-energetic images improve the generalization of an FCN used for myocardium segmentation in CCTA images.
Automatic segmentation of left ventricle (LV) myocardium in cardiac short-axis cine MR images acquired on subjects with myocardial infarction is a challenging task, mainly because of the various types of image inhomogeneity caused by the infarctions. Among the approaches proposed to automate the LV myocardium segmentation task, methods based upon deep convolutional neural networks (CNN) have demonstrated their exceptional accuracy and robustness in recent years. However, most of the CNN-based approaches treat the frames in a cardiac cycle independently, which fails to capture the valuable dynamics of heart motion. Herein, an approach based on recurrent neural network (RNN), specifically a multi-level convolutional long short-term memory (ConvLSTM) model, is proposed to take the motion of the heart into consideration. Based on a ResNet-56 CNN, LV-related image features in consecutive frames of a cardiac cycle are extracted at both the low- and high-resolution levels, which are processed by the corresponding multi-level ConvLSTM models to generate the myocardium segmentations. A leave-one-out experiment was carried out on a set of 3,600 cardiac cine MR slices collected in-house for 8 porcine subjects with surgically induced myocardial infarction. Compared with a solely CNN-based approach, the proposed approach demonstrated its superior robustness against image inhomogeneity by incorporating information from adjacent frames. It also outperformed a one-level ConvLSTM approach thanks to its capabilities to take advantage of image features at multiple resolution levels.
Segmentation of the left ventricle and quantification of various cardiac contractile functions is crucial for the timely diagnosis and treatment of cardiovascular diseases. Traditionally, the two tasks have been tackled independently. Here we propose a convolutional neural network based multi-task learning approach to perform both tasks simultaneously, such that, the network learns better representation of the data with improved generalization performance. Probabilistic formulation of the problem enables learning the task uncertainties during the training, which are used to automatically compute the weights for the tasks. We performed a five fold cross-validation of the myocardium segmentation obtained from the proposed multi-task network on 97 patient 4-dimensional cardiac cine-MRI datasets available through the STACOM LV segmentation challenge against the provided gold-standard myocardium segmentation, obtaining a Dice overlap of $0.849 \pm 0.036$ and mean surface distance of $0.274 \pm 0.083$ mm, while simultaneously estimating the myocardial area with mean absolute difference error of $205\pm198$ mm$^2$.