Qi Yang

Xin Yu, Qi Yang, Yucheng Tang et al.

2D low-dose single-slice abdominal computed tomography (CT) slice enables direct measurements of body composition, which are critical to quantitatively characterizing health relationships on aging. However, longitudinal analysis of body composition changes using 2D abdominal slices is challenging due to positional variance between longitudinal slices acquired in different years. To reduce the positional variance, we extend the conditional generative models to our C-SliceGen that takes an arbitrary axial slice in the abdominal region as the condition and generates a defined vertebral level slice by estimating the structural changes in the latent space. Experiments on 1170 subjects from an in-house dataset and 50 subjects from BTCV MICCAI Challenge 2015 show that our model can generate high quality images in terms of realism and similarity. External experiments on 20 subjects from the Baltimore Longitudinal Study of Aging (BLSA) dataset that contains longitudinal single abdominal slices validate that our method can harmonize the slice positional variance in terms of muscle and visceral fat area. Our approach provides a promising direction of mapping slices from different vertebral levels to a target slice to reduce positional variance for single slice longitudinal analysis. The source code is available at: https://github.com/MASILab/C-SliceGen.

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

Ho Hin Lee, Yucheng Tang, Riqiang Gao et al.

Non-contrast computed tomography (NCCT) is commonly acquired for lung cancer screening, assessment of general abdominal pain or suspected renal stones, trauma evaluation, and many other indications. However, the absence of contrast limits distinguishing organ in-between boundaries. In this paper, we propose a novel unsupervised approach that leverages pairwise contrast-enhanced CT (CECT) context to compute non-contrast segmentation without ground-truth label. Unlike generative adversarial approaches, we compute the pairwise morphological context with CECT to provide teacher guidance instead of generating fake anatomical context. Additionally, we further augment the intensity correlations in 'organ-specific' settings and increase the sensitivity to organ-aware boundary. We validate our approach on multi-organ segmentation with paired non-contrast & contrast-enhanced CT scans using five-fold cross-validation. Full external validations are performed on an independent non-contrast cohort for aorta segmentation. Compared with current abdominal organs segmentation state-of-the-art in fully supervised setting, our proposed pipeline achieves a significantly higher Dice by 3.98% (internal multi-organ annotated), and 8.00% (external aorta annotated) for abdominal organs segmentation. The code and pretrained models are publicly available at https://github.com/MASILab/ContrastMix.

Ho Hin Lee, Yucheng Tang, Han Liu et al.

Recent studies have demonstrated the superior performance of introducing ``scan-wise" contrast labels into contrastive learning for multi-organ segmentation on multi-phase computed tomography (CT). However, such scan-wise labels are limited: (1) a coarse classification, which could not capture the fine-grained ``organ-wise" contrast variations across all organs; (2) the label (i.e., contrast phase) is typically manually provided, which is error-prone and may introduce manual biases of defining phases. In this paper, we propose a novel data-driven contrastive loss function that adapts the similar/dissimilar contrast relationship between samples in each minibatch at organ-level. Specifically, as variable levels of contrast exist between organs, we hypothesis that the contrast differences in the organ-level can bring additional context for defining representations in the latent space. An organ-wise contrast correlation matrix is computed with mean organ intensities under one-hot attention maps. The goal of adapting the organ-driven correlation matrix is to model variable levels of feature separability at different phases. We evaluate our proposed approach on multi-organ segmentation with both non-contrast CT (NCCT) datasets and the MICCAI 2015 BTCV Challenge contrast-enhance CT (CECT) datasets. Compared to the state-of-the-art approaches, our proposed contrastive loss yields a substantial and significant improvement of 1.41% (from 0.923 to 0.936, p-value$<$0.01) and 2.02% (from 0.891 to 0.910, p-value$<$0.01) on mean Dice scores across all organs with respect to NCCT and CECT cohorts. We further assess the trained model performance with the MICCAI 2021 FLARE Challenge CECT datasets and achieve a substantial improvement of mean Dice score from 0.927 to 0.934 (p-value$<$0.01). The code is available at: https://github.com/MASILab/DCC_CL

Xin Yu, Yucheng Tang, Qi Yang et al.

Metabolic health is increasingly implicated as a risk factor across conditions from cardiology to neurology, and efficiency assessment of body composition is critical to quantitatively characterizing these relationships. 2D low dose single slice computed tomography (CT) provides a high resolution, quantitative tissue map, albeit with a limited field of view. Although numerous potential analyses have been proposed in quantifying image context, there has been no comprehensive study for low-dose single slice CT longitudinal variability with automated segmentation. We studied a total of 1816 slices from 1469 subjects of Baltimore Longitudinal Study on Aging (BLSA) abdominal dataset using supervised deep learning-based segmentation and unsupervised clustering method. 300 out of 1469 subjects that have two year gap in their first two scans were pick out to evaluate longitudinal variability with measurements including intraclass correlation coefficient (ICC) and coefficient of variation (CV) in terms of tissues/organs size and mean intensity. We showed that our segmentation methods are stable in longitudinal settings with Dice ranged from 0.821 to 0.962 for thirteen target abdominal tissues structures. We observed high variability in most organ with ICC<0.5, low variability in the area of muscle, abdominal wall, fat and body mask with average ICC>0.8. We found that the variability in organ is highly related to the cross-sectional position of the 2D slice. Our efforts pave quantitative exploration and quality control to reduce uncertainties in longitudinal analysis.

Chenyu Gao, Michael E. Kim, Ho Hin Lee et al.

Imaging findings inconsistent with those expected at specific chronological age ranges may serve as early indicators of neurological disorders and increased mortality risk. Estimation of chronological age, and deviations from expected results, from structural MRI data has become an important task for developing biomarkers that are sensitive to such deviations. Complementary to structural analysis, diffusion tensor imaging (DTI) has proven effective in identifying age-related microstructural changes within the brain white matter, thereby presenting itself as a promising additional modality for brain age prediction. Although early studies have sought to harness DTI's advantages for age estimation, there is no evidence that the success of this prediction is owed to the unique microstructural and diffusivity features that DTI provides, rather than the macrostructural features that are also available in DTI data. Therefore, we seek to develop white-matter-specific age estimation to capture deviations from normal white matter aging. Specifically, we deliberately disregard the macrostructural information when predicting age from DTI scalar images, using two distinct methods. The first method relies on extracting only microstructural features from regions of interest. The second applies 3D residual neural networks (ResNets) to learn features directly from the images, which are non-linearly registered and warped to a template to minimize macrostructural variations. When tested on unseen data, the first method yields mean absolute error (MAE) of 6.11 years for cognitively normal participants and MAE of 6.62 years for cognitively impaired participants, while the second method achieves MAE of 4.69 years for cognitively normal participants and MAE of 4.96 years for cognitively impaired participants. We find that the ResNet model captures subtler, non-macrostructural features for brain age prediction.

Yinchi Zhou, Ho Hin Lee, Yucheng Tang et al.

With the substantial diversity in population demographics, such as differences in age and body composition, the volumetric morphology of pancreas varies greatly, resulting in distinctive variations in shape and appearance. Such variations increase the difficulty at generalizing population-wide pancreas features. A volumetric spatial reference is needed to adapt the morphological variability for organ-specific analysis. Here, we proposed a high-resolution computed tomography (CT) atlas framework specifically optimized for the pancreas organ across multi-contrast CT. We introduce a deep learning-based pre-processing technique to extract the abdominal region of interests (ROIs) and leverage a hierarchical registration pipeline to align the pancreas anatomy across populations. Briefly, DEEDs affine and non-rigid registration are performed to transfer patient abdominal volumes to a fixed high-resolution atlas template. To generate and evaluate the pancreas atlas template, multi-contrast modality CT scans of 443 subjects (without reported history of pancreatic disease, age: 15-50 years old) are processed. Comparing with different registration state-of-the-art tools, the combination of DEEDs affine and non-rigid registration achieves the best performance for the pancreas label transfer across all contrast phases. We further perform external evaluation with another research cohort of 100 de-identified portal venous scans with 13 organs labeled, having the best label transfer performance of 0.504 Dice score in unsupervised setting. The qualitative representation (e.g., average mapping) of each phase creates a clear boundary of pancreas and its distinctive contrast appearance. The deformation surface renderings across scales (e.g., small to large volume) further illustrate the generalizability of the proposed atlas template.

Qi Yang, Yipeng Liu, Siheng Chen et al.

We present a novel no-reference quality assessment metric, the image transferred point cloud quality assessment (IT-PCQA), for 3D point clouds. For quality assessment, deep neural network (DNN) has shown compelling performance on no-reference metric design. However, the most challenging issue for no-reference PCQA is that we lack large-scale subjective databases to drive robust networks. Our motivation is that the human visual system (HVS) is the decision-maker regardless of the type of media for quality assessment. Leveraging the rich subjective scores of the natural images, we can quest the evaluation criteria of human perception via DNN and transfer the capability of prediction to 3D point clouds. In particular, we treat natural images as the source domain and point clouds as the target domain, and infer point cloud quality via unsupervised adversarial domain adaptation. To extract effective latent features and minimize the domain discrepancy, we propose a hierarchical feature encoder and a conditional-discriminative network. Considering that the ultimate purpose is regressing objective score, we introduce a novel conditional cross entropy loss in the conditional-discriminative network to penalize the negative samples which hinder the convergence of the quality regression network. Experimental results show that the proposed method can achieve higher performance than traditional no-reference metrics, even comparable results with full-reference metrics. The proposed method also suggests the feasibility of assessing the quality of specific media content without the expensive and cumbersome subjective evaluations. Code is available at https://github.com/Qi-Yangsjtu/IT-PCQA.

Chenyu Gao, Michael E. Kim, Karthik Ramadass et al.

Estimated brain age from magnetic resonance image (MRI) and its deviation from chronological age can provide early insights into potential neurodegenerative diseases, supporting early detection and implementation of prevention strategies. Diffusion MRI (dMRI) presents an opportunity to build an earlier biomarker for neurodegenerative disease prediction because it captures subtle microstructural changes that precede more perceptible macrostructural changes. However, the coexistence of macro- and micro-structural information in dMRI raises the question of whether current dMRI-based brain age estimation models are leveraging the intended microstructural information or if they inadvertently rely on the macrostructural information. To develop a microstructure-specific brain age, we propose a method for brain age identification from dMRI that mitigates the model's use of macrostructural information by non-rigidly registering all images to a standard template. Imaging data from 13,398 participants across 12 datasets were used for the training and evaluation. We compare our brain age models, trained with and without macrostructural information mitigated, with an architecturally similar T1-weighted (T1w) MRI-based brain age model and two recent, popular, openly available T1w MRI-based brain age models that primarily use macrostructural information. We observe difference between our dMRI-based brain age and T1w MRI-based brain age across stages of neurodegeneration, with dMRI-based brain age being older than T1w MRI-based brain age in participants transitioning from cognitively normal (CN) to mild cognitive impairment (MCI), but younger in participants already diagnosed with Alzheimer's disease (AD). Furthermore, dMRI-based brain age may offer advantages over T1w MRI-based brain age in predicting the transition from CN to MCI up to five years before diagnosis.

Ho Hin Lee, Adam M. Saunders, Michael E. Kim et al.

Purpose: Eye morphology varies significantly across the population, especially for the orbit and optic nerve. These variations limit the feasibility and robustness of generalizing population-wise features of eye organs to an unbiased spatial reference. Approach: To tackle these limitations, we propose a process for creating high-resolution unbiased eye atlases. First, to restore spatial details from scans with a low through-plane resolution compared to a high in-plane resolution, we apply a deep learning-based super-resolution algorithm. Then, we generate an initial unbiased reference with an iterative metric-based registration using a small portion of subject scans. We register the remaining scans to this template and refine the template using an unsupervised deep probabilistic approach that generates a more expansive deformation field to enhance the organ boundary alignment. We demonstrate this framework using magnetic resonance images across four different tissue contrasts, generating four atlases in separate spatial alignments. Results: For each tissue contrast, we find a significant improvement using the Wilcoxon signed-rank test in the average Dice score across four labeled regions compared to a standard registration framework consisting of rigid, affine, and deformable transformations. These results highlight the effective alignment of eye organs and boundaries using our proposed process. Conclusions: By combining super-resolution preprocessing and deep probabilistic models, we address the challenge of generating an eye atlas to serve as a standardized reference across a largely variable population.

Xin Yu, Qi Yang, Han Liu et al.

2D single-slice abdominal computed tomography (CT) enables the assessment of body habitus and organ health with low radiation exposure. However, single-slice data necessitates the use of 2D networks for segmentation, but these networks often struggle to capture contextual information effectively. Consequently, even when trained on identical datasets, 3D networks typically achieve superior segmentation results. In this work, we propose a novel 3D-to-2D distillation framework, leveraging pre-trained 3D models to enhance 2D single-slice segmentation. Specifically, we extract the prediction distribution centroid from the 3D representations, to guide the 2D student by learning intra- and inter-class correlation. Unlike traditional knowledge distillation methods that require the same data input, our approach employs unpaired 3D CT scans with any contrast to guide the 2D student model. Experiments conducted on 707 subjects from the single-slice Baltimore Longitudinal Study of Aging (BLSA) dataset demonstrate that state-of-the-art 2D multi-organ segmentation methods can benefit from the 3D teacher model, achieving enhanced performance in single-slice multi-organ segmentation. Notably, our approach demonstrates considerable efficacy in low-data regimes, outperforming the model trained with all available training subjects even when utilizing only 200 training subjects. Thus, this work underscores the potential to alleviate manual annotation burdens.

Ho Hin Lee, Yucheng Tang, Qi Yang et al.

Medical image segmentation, or computing voxelwise semantic masks, is a fundamental yet challenging task to compute a voxel-level semantic mask. To increase the ability of encoder-decoder neural networks to perform this task across large clinical cohorts, contrastive learning provides an opportunity to stabilize model initialization and enhance encoders without labels. However, multiple target objects (with different semantic meanings) may exist in a single image, which poses a problem for adapting traditional contrastive learning methods from prevalent 'image-level classification' to 'pixel-level segmentation'. In this paper, we propose a simple semantic-aware contrastive learning approach leveraging attention masks to advance multi-object semantic segmentation. Briefly, we embed different semantic objects to different clusters rather than the traditional image-level embeddings. We evaluate our proposed method on a multi-organ medical image segmentation task with both in-house data and MICCAI Challenge 2015 BTCV datasets. Compared with current state-of-the-art training strategies, our proposed pipeline yields a substantial improvement of 5.53% and 6.09% on Dice score for both medical image segmentation cohorts respectively (p-value<0.01). The performance of the proposed method is further assessed on natural images via the PASCAL VOC 2012 dataset, and achieves a substantial improvement of 2.75% on mIoU (p-value<0.01).

Qi Yang, Zhan Ma, Yiling Xu et al.

We propose the GraphSIM -- an objective metric to accurately predict the subjective quality of point cloud with superimposed geometry and color impairments. Motivated by the facts that human vision system is more sensitive to the high spatial-frequency components (e.g., contours, edges), and weighs more to the local structural variations rather individual point intensity, we first extract geometric keypoints by resampling the reference point cloud geometry information to form the object skeleton; we then construct local graphs centered at these keypoints for both reference and distorted point clouds, followed by collectively aggregating color gradient moments (e.g., zeroth, first, and second) that are derived between all other points and centered keypoint in the same local graph for significant feature similarity (a.k.a., local significance) measurement; Final similarity index is obtained by pooling the local graph significance across all color channels and by averaging across all graphs. Our GraphSIM is validated using two large and independent point cloud assessment datasets that involve a wide range of impairments (e.g., re-sampling, compression, additive noise), reliably demonstrating the state-of-the-art performance for all distortions with noticeable gains in predicting the subjective mean opinion score (MOS), compared with those point-wise distance-based metrics adopted in standardization reference software. Ablation studies have further shown that GraphSIM is generalized to various scenarios with consistent performance by examining its key modules and parameters.

Xi Ouyang, Jiayu Huo, Liming Xia et al.

The coronavirus disease (COVID-19) is rapidly spreading all over the world, and has infected more than 1,436,000 people in more than 200 countries and territories as of April 9, 2020. Detecting COVID-19 at early stage is essential to deliver proper healthcare to the patients and also to protect the uninfected population. To this end, we develop a dual-sampling attention network to automatically diagnose COVID- 19 from the community acquired pneumonia (CAP) in chest computed tomography (CT). In particular, we propose a novel online attention module with a 3D convolutional network (CNN) to focus on the infection regions in lungs when making decisions of diagnoses. Note that there exists imbalanced distribution of the sizes of the infection regions between COVID-19 and CAP, partially due to fast progress of COVID-19 after symptom onset. Therefore, we develop a dual-sampling strategy to mitigate the imbalanced learning. Our method is evaluated (to our best knowledge) upon the largest multi-center CT data for COVID-19 from 8 hospitals. In the training-validation stage, we collect 2186 CT scans from 1588 patients for a 5-fold cross-validation. In the testing stage, we employ another independent large-scale testing dataset including 2796 CT scans from 2057 patients. Results show that our algorithm can identify the COVID-19 images with the area under the receiver operating characteristic curve (AUC) value of 0.944, accuracy of 87.5%, sensitivity of 86.9%, specificity of 90.1%, and F1-score of 82.0%. With this performance, the proposed algorithm could potentially aid radiologists with COVID-19 diagnosis from CAP, especially in the early stage of the COVID-19 outbreak.