Kaiwen Xu

Thomas Z. Li, Kaiwen Xu, Riqiang Gao et al.

Features learned from single radiologic images are unable to provide information about whether and how much a lesion may be changing over time. Time-dependent features computed from repeated images can capture those changes and help identify malignant lesions by their temporal behavior. However, longitudinal medical imaging presents the unique challenge of sparse, irregular time intervals in data acquisition. While self-attention has been shown to be a versatile and efficient learning mechanism for time series and natural images, its potential for interpreting temporal distance between sparse, irregularly sampled spatial features has not been explored. In this work, we propose two interpretations of a time-distance vision transformer (ViT) by using (1) vector embeddings of continuous time and (2) a temporal emphasis model to scale self-attention weights. The two algorithms are evaluated based on benign versus malignant lung cancer discrimination of synthetic pulmonary nodules and lung screening computed tomography studies from the National Lung Screening Trial (NLST). Experiments evaluating the time-distance ViTs on synthetic nodules show a fundamental improvement in classifying irregularly sampled longitudinal images when compared to standard ViTs. In cross-validation on screening chest CTs from the NLST, our methods (0.785 and 0.786 AUC respectively) significantly outperform a cross-sectional approach (0.734 AUC) and match the discriminative performance of the leading longitudinal medical imaging algorithm (0.779 AUC) on benign versus malignant classification. This work represents the first self-attention-based framework for classifying longitudinal medical images. Our code is available at https://github.com/tom1193/time-distance-transformer.

Qi Yang, Xin Yu, Ho Hin Lee et al.

Objective: Thigh muscle group segmentation is important for assessment of muscle anatomy, metabolic disease and aging. Many efforts have been put into quantifying muscle tissues with magnetic resonance (MR) imaging including manual annotation of individual muscles. However, leveraging publicly available annotations in MR images to achieve muscle group segmentation on single slice computed tomography (CT) thigh images is challenging. Method: We propose an unsupervised domain adaptation pipeline with self-training to transfer labels from 3D MR to single CT slice. First, we transform the image appearance from MR to CT with CycleGAN and feed the synthesized CT images to a segmenter simultaneously. Single CT slices are divided into hard and easy cohorts based on the entropy of pseudo labels inferenced by the segmenter. After refining easy cohort pseudo labels based on anatomical assumption, self-training with easy and hard splits is applied to fine tune the segmenter. Results: On 152 withheld single CT thigh images, the proposed pipeline achieved a mean Dice of 0.888(0.041) across all muscle groups including sartorius, hamstrings, quadriceps femoris and gracilis. muscles Conclusion: To our best knowledge, this is the first pipeline to achieve thigh imaging domain adaptation from MR to CT. The proposed pipeline is effective and robust in extracting muscle groups on 2D single slice CT thigh images.The container is available for public use at https://github.com/MASILab/DA_CT_muscle_seg

Kaiwen Xu, Thomas Li, Mirza S. Khan et al.

Field-of-view (FOV) tissue truncation beyond the lungs is common in routine lung screening computed tomography (CT). This poses limitations for opportunistic CT- based body composition (BC) assessment as key anatomical structures are missing. Traditionally, extending the FOV of CT is considered as a CT reconstruction problem using limited data. However, this approach relies on the projection domain data which might not be available in application. In this work, we formulate the problem from the semantic image extension perspective which only requires image data as inputs. The proposed two-stage method identifies a new FOV border based on the estimated extent of the complete body and imputes missing tissues in the truncated region. The training samples are simulated using CT slices with complete body in FOV, making the model development self-supervised. We evaluate the validity of the proposed method in automatic BC assessment using lung screening CT with limited FOV. The proposed method effectively restores the missing tissues and reduces BC assessment error introduced by FOV tissue truncation. In the BC assessment for a large-scale lung screening CT dataset, this correction improves both the intra-subject consistency and the correlation with anthropometric approximations. The developed method is available at https://github.com/MASILab/S-EFOV.

Thomas Z. Li, John M. Still, Kaiwen Xu et al.

The accuracy of predictive models for solitary pulmonary nodule (SPN) diagnosis can be greatly increased by incorporating repeat imaging and medical context, such as electronic health records (EHRs). However, clinically routine modalities such as imaging and diagnostic codes can be asynchronous and irregularly sampled over different time scales which are obstacles to longitudinal multimodal learning. In this work, we propose a transformer-based multimodal strategy to integrate repeat imaging with longitudinal clinical signatures from routinely collected EHRs for SPN classification. We perform unsupervised disentanglement of latent clinical signatures and leverage time-distance scaled self-attention to jointly learn from clinical signatures expressions and chest computed tomography (CT) scans. Our classifier is pretrained on 2,668 scans from a public dataset and 1,149 subjects with longitudinal chest CTs, billing codes, medications, and laboratory tests from EHRs of our home institution. Evaluation on 227 subjects with challenging SPNs revealed a significant AUC improvement over a longitudinal multimodal baseline (0.824 vs 0.752 AUC), as well as improvements over a single cross-section multimodal scenario (0.809 AUC) and a longitudinal imaging-only scenario (0.741 AUC). This work demonstrates significant advantages with a novel approach for co-learning longitudinal imaging and non-imaging phenotypes with transformers. Code available at https://github.com/MASILab/lmsignatures.

Kaiwen Xu, Aravind R. Krishnan, Thomas Z. Li et al.

Anatomically consistent field-of-view (FOV) completion to recover truncated body sections has important applications in quantitative analyses of computed tomography (CT) with limited FOV. Existing solution based on conditional generative models relies on the fidelity of synthetic truncation patterns at training phase, which poses limitations for the generalizability of the method to potential unknown types of truncation. In this study, we evaluate a zero-shot method based on a pretrained unconditional generative diffusion prior, where truncation pattern with arbitrary forms can be specified at inference phase. In evaluation on simulated chest CT slices with synthetic FOV truncation, the method is capable of recovering anatomically consistent body sections and subcutaneous adipose tissue measurement error caused by FOV truncation. However, the correction accuracy is inferior to the conditionally trained counterpart.

Chenyu Gao, Kaiwen Xu, Michael E. Kim et al.

Defacing is often applied to head magnetic resonance image (MRI) datasets prior to public release to address privacy concerns. The alteration of facial and nearby voxels has provoked discussions about the true capability of these techniques to ensure privacy as well as their impact on downstream tasks. With advancements in deep generative models, the extent to which defacing can protect privacy is uncertain. Additionally, while the altered voxels are known to contain valuable anatomical information, their potential to support research beyond the anatomical regions directly affected by defacing remains uncertain. To evaluate these considerations, we develop a refacing pipeline that recovers faces in defaced head MRIs using cascaded diffusion probabilistic models (DPMs). The DPMs are trained on images from 180 subjects and tested on images from 484 unseen subjects, 469 of whom are from a different dataset. To assess whether the altered voxels in defacing contain universally useful information, we also predict computed tomography (CT)-derived skeletal muscle radiodensity from facial voxels in both defaced and original MRIs. The results show that DPMs can generate high-fidelity faces that resemble the original faces from defaced images, with surface distances to the original faces significantly smaller than those of a population average face (p < 0.05). This performance also generalizes well to previously unseen datasets. For skeletal muscle radiodensity predictions, using defaced images results in significantly weaker Spearman's rank correlation coefficients compared to using original images (p < 10-4). For shin muscle, the correlation is statistically significant (p < 0.05) when using original images but not statistically significant (p > 0.05) when any defacing method is applied, suggesting that defacing might not only fail to protect privacy but also eliminate valuable information.

Lianrui Zuo, Kaiwen Xu, Dingjie Su et al.

The interconnection between the human lungs and other organs, such as the liver and kidneys, is crucial for understanding the underlying risks and effects of lung diseases and improving patient care. However, most research chest CT imaging is focused solely on the lungs due to considerations of cost and radiation dose. This restricted field of view (FOV) in the acquired images poses challenges to comprehensive analysis and hinders the ability to gain insights into the impact of lung diseases on other organs. To address this, we propose SCOPE (Spatial Coverage Optimization with Prior Encoding), a novel approach to capture the inter-organ relationships from CT images and extend the FOV of chest CT images. Our approach first trains a variational autoencoder (VAE) to encode 2D axial CT slices individually, then stacks the latent representations of the VAE to form a 3D context for training a latent diffusion model. Once trained, our approach extends the FOV of CT images in the z-direction by generating new axial slices in a zero-shot manner. We evaluated our approach on the National Lung Screening Trial (NLST) dataset, and results suggest that it effectively extends the FOV to include the liver and kidneys, which are not completely covered in the original NLST data acquisition. Quantitative results on a held-out whole-body dataset demonstrate that the generated slices exhibit high fidelity with acquired data, achieving an SSIM of 0.81.

Suma Anand, Kaiwen Xu, Colm O'Dushlaine et al.

Magnetic Resonance Imaging (MRI) is the gold standard for measuring fat and iron content non-invasively in the body via measures known as Proton Density Fat Fraction (PDFF) and $R_2^*$, respectively. However, conventional PDFF and $R_2^*$ quantification methods operate on MR images voxel-wise and require at least three measurements to estimate three quantities: water, fat, and $R_2^*$. Alternatively, the two-point Dixon MRI protocol is widely used and fast because it acquires only two measurements; however, these cannot be used to estimate three quantities voxel-wise. Leveraging the fact that neighboring voxels have similar values, we propose using a generative machine learning approach to learn PDFF and $R_2^*$ from Dixon MRI. We use paired Dixon-IDEAL data from UK Biobank in the liver and a Pix2Pix conditional GAN to demonstrate the first large-scale $R_2^*$ imputation from two-point Dixon MRIs. Using our proposed approach, we synthesize PDFF and $R_2^*$ maps that show significantly greater correlation with ground-truth than conventional voxel-wise baselines.

Ho Hin Lee, Yucheng Tang, Kaiwen Xu et al.

The construction of three-dimensional multi-modal tissue maps provides an opportunity to spur interdisciplinary innovations across temporal and spatial scales through information integration. While the preponderance of effort is allocated to the cellular level and explore the changes in cell interactions and organizations, contextualizing findings within organs and systems is essential to visualize and interpret higher resolution linkage across scales. There is a substantial normal variation of kidney morphometry and appearance across body size, sex, and imaging protocols in abdominal computed tomography (CT). A volumetric atlas framework is needed to integrate and visualize the variability across scales. However, there is no abdominal and retroperitoneal organs atlas framework for multi-contrast CT. Hence, we proposed a high-resolution CT retroperitoneal atlas specifically optimized for the kidney across non-contrast CT and early arterial, late arterial, venous and delayed contrast enhanced CT. Briefly, we introduce a deep learning-based volume of interest extraction method and an automated two-stage hierarchal registration pipeline to register abdominal volumes to a high-resolution CT atlas template. To generate and evaluate the atlas, multi-contrast modality CT scans of 500 subjects (without reported history of renal disease, age: 15-50 years, 250 males & 250 females) were processed. We demonstrate a stable generalizability of the atlas template for integrating the normal kidney variation from small to large, across contrast modalities and populations with great variability of demographics. The linkage of atlas and demographics provided a better understanding of the variation of kidney anatomy across populations.