Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.
In this work, we developed a novel text-guided image synthesis technique which could generate realistic tau PET images from textual descriptions and the subject's MR image. The generated tau PET images have the potential to be used in examining relations between different measures and also increasing the public availability of tau PET datasets. The method was based on latent diffusion models. Both textual descriptions and the subject's MR prior image were utilized as conditions during image generation. The subject's MR image can provide anatomical details, while the text descriptions, such as gender, scan time, cognitive test scores, and amyloid status, can provide further guidance regarding where the tau neurofibrillary tangles might be deposited. Preliminary experimental results based on clinical [18F]MK-6240 datasets demonstrate the feasibility of the proposed method in generating realistic tau PET images at different clinical stages.
Radiotherapy (RT) combined with cetuximab is the standard treatment for patients with inoperable head and neck cancers. Segmentation of head and neck (H&N) tumors is a prerequisite for radiotherapy planning but a time-consuming process. In recent years, deep convolutional neural networks have become the de facto standard for automated image segmentation. However, due to the expensive computational cost associated with enlarging the field of view in DCNNs, their ability to model long-range dependency is still limited, and this can result in sub-optimal segmentation performance for objects with background context spanning over long distances. On the other hand, Transformer models have demonstrated excellent capabilities in capturing such long-range information in several semantic segmentation tasks performed on medical images. Inspired by the recent success of Vision Transformers and advances in multi-modal image analysis, we propose a novel segmentation model, debuted, Cross-Modal Swin Transformer (SwinCross), with cross-modal attention (CMA) module to incorporate cross-modal feature extraction at multiple resolutions.To validate the effectiveness of the proposed method, we performed experiments on the HECKTOR 2021 challenge dataset and compared it with the nnU-Net (the backbone of the top-5 methods in HECKTOR 2021) and other state-of-the-art transformer-based methods such as UNETR, and Swin UNETR. The proposed method is experimentally shown to outperform these comparing methods thanks to the ability of the CMA module to capture better inter-modality complimentary feature representations between PET and CT, for the task of head-and-neck tumor segmentation.
Inspired by the recent success of Transformers for Natural Language Processing and vision Transformer for Computer Vision, many researchers in the medical imaging community have flocked to Transformer-based networks for various main stream medical tasks such as classification, segmentation, and estimation. In this study, we analyze, two recently published Transformer-based network architectures for the task of multimodal head-and-tumor segmentation and compare their performance to the de facto standard 3D segmentation network - the nnU-Net. Our results showed that modeling long-range dependencies may be helpful in cases where large structures are present and/or large field of view is needed. However, for small structures such as head-and-neck tumor, the convolution-based U-Net architecture seemed to perform well, especially when training dataset is small and computational resource is limited.
Due to various physical degradation factors and limited counts received, PET image quality needs further improvements. The denoising diffusion probabilistic models (DDPM) are distribution learning-based models, which try to transform a normal distribution into a specific data distribution based on iterative refinements. In this work, we proposed and evaluated different DDPM-based methods for PET image denoising. Under the DDPM framework, one way to perform PET image denoising is to provide the PET image and/or the prior image as the network input. Another way is to supply the prior image as the input with the PET image included in the refinement steps, which can fit for scenarios of different noise levels. 120 18F-FDG datasets and 140 18F-MK-6240 datasets were utilized to evaluate the proposed DDPM-based methods. Quantification show that the DDPM-based frameworks with PET information included can generate better results than the nonlocal mean and Unet-based denoising methods. Adding additional MR prior in the model can help achieve better performance and further reduce the uncertainty during image denoising. Solely relying on MR prior while ignoring the PET information can result in large bias. Regional and surface quantification shows that employing MR prior as the network input while embedding PET image as a data-consistency constraint during inference can achieve the best performance. In summary, DDPM-based PET image denoising is a flexible framework, which can efficiently utilize prior information and achieve better performance than the nonlocal mean and Unet-based denoising methods.
Position emission tomography (PET) is widely used in clinics and research due to its quantitative merits and high sensitivity, but suffers from low signal-to-noise ratio (SNR). Recently convolutional neural networks (CNNs) have been widely used to improve PET image quality. Though successful and efficient in local feature extraction, CNN cannot capture long-range dependencies well due to its limited receptive field. Global multi-head self-attention (MSA) is a popular approach to capture long-range information. However, the calculation of global MSA for 3D images has high computational costs. In this work, we proposed an efficient spatial and channel-wise encoder-decoder transformer, Spach Transformer, that can leverage spatial and channel information based on local and global MSAs. Experiments based on datasets of different PET tracers, i.e., $^{18}$F-FDG, $^{18}$F-ACBC, $^{18}$F-DCFPyL, and $^{68}$Ga-DOTATATE, were conducted to evaluate the proposed framework. Quantitative results show that the proposed Spach Transformer can achieve better performance than other reference methods.
In PET, the amount of relative (signal-dependent) noise present in different body regions can be significantly different and is inherently related to the number of counts present in that region. The number of counts in a region depends, in principle and among other factors, on the total administered activity, scanner sensitivity, image acquisition duration, radiopharmaceutical tracer uptake in the region, and patient local body morphometry surrounding the region. In theory, less amount of denoising operations is needed to denoise a high-count (low relative noise) image than images a low-count (high relative noise) image, and vice versa. The current deep-learning-based methods for PET image denoising are predominantly trained on image appearance only and have no special treatment for images of different noise levels. Our hypothesis is that by explicitly providing the local relative noise level of the input image to a deep convolutional neural network (DCNN), the DCNN can outperform itself trained on image appearance only. To this end, we propose a noise-level-aware framework denoising framework that allows embedding of local noise level into a DCNN. The proposed is trained and tested on 30 and 15 patient PET images acquired on a GE Discovery MI PET/CT system. Our experiments showed that the increases in both PSNR and SSIM from our backbone network with relative noise level embedding (NLE) versus the same network without NLE were statistically significant with p<0.001, and the proposed method significantly outperformed a strong baseline method by a large margin.
Image reconstruction of low-count positron emission tomography (PET) data is challenging. Kernel methods address the challenge by incorporating image prior information in the forward model of iterative PET image reconstruction. The kernelized expectation-maximization (KEM) algorithm has been developed and demonstrated to be effective and easy to implement. A common approach for a further improvement of the kernel method would be adding an explicit regularization, which however leads to a complex optimization problem. In this paper, we propose an implicit regularization for the kernel method by using a deep coefficient prior, which represents the kernel coefficient image in the PET forward model using a convolutional neural-network. To solve the maximum-likelihood neural network-based reconstruction problem, we apply the principle of optimization transfer to derive a neural KEM algorithm. Each iteration of the algorithm consists of two separate steps: a KEM step for image update from the projection data and a deep-learning step in the image domain for updating the kernel coefficient image using the neural network. This optimization algorithm is guaranteed to monotonically increase the data likelihood. The results from computer simulations and real patient data have demonstrated that the neural KEM can outperform existing KEM and deep image prior methods.
Direct reconstruction methods have been developed to estimate parametric images directly from the measured PET sinograms by combining the PET imaging model and tracer kinetics in an integrated framework. Due to limited counts received, signal-to-noise-ratio (SNR) and resolution of parametric images produced by direct reconstruction frameworks are still limited. Recently supervised deep learning methods have been successfully applied to medical imaging denoising/reconstruction when large number of high-quality training labels are available. For static PET imaging, high-quality training labels can be acquired by extending the scanning time. However, this is not feasible for dynamic PET imaging, where the scanning time is already long enough. In this work, we proposed an unsupervised deep learning framework for direct parametric reconstruction from dynamic PET, which was tested on the Patlak model and the relative equilibrium Logan model. The patient's anatomical prior image, which is readily available from PET/CT or PET/MR scans, was supplied as the network input to provide a manifold constraint, and also utilized to construct a kernel layer to perform non-local feature denoising. The linear kinetic model was embedded in the network structure as a 1x1 convolution layer. The training objective function was based on the PET statistical model. Evaluations based on dynamic datasets of 18F-FDG and 11C-PiB tracers show that the proposed framework can outperform the traditional and the kernel method-based direct reconstruction methods.
Arterial spin labeling (ASL) magnetic resonance imaging (MRI) is a powerful imaging technology that can measure cerebral blood flow (CBF) quantitatively. However, since only a small portion of blood is labeled compared to the whole tissue volume, conventional ASL suffers from low signal-to-noise ratio (SNR), poor spatial resolution, and long acquisition time. In this paper, we proposed a super-resolution method based on a multi-scale generative adversarial network (GAN) through unsupervised training. The network only needs the low-resolution (LR) ASL image itself for training and the T1-weighted image as the anatomical prior. No training pairs or pre-training are needed. A low-pass filter guided item was added as an additional loss to suppress the noise interference from the LR ASL image. After the network was trained, the super-resolution (SR) image was generated by supplying the upsampled LR ASL image and corresponding T1-weighted image to the generator of the last layer. Performance of the proposed method was evaluated by comparing the peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM) using normal-resolution (NR) ASL image (5.5 min acquisition) and high-resolution (HR) ASL image (44 min acquisition) as the ground truth. Compared to the nearest, linear, and spline interpolation methods, the proposed method recovers more detailed structure information, reduces the image noise visually, and achieves the highest PSNR and SSIM when using HR ASL image as the ground-truth.