Yang Lei

Huiqiao Xie, Yang Lei, Yabo Fu et al.

CBCTs in image-guided radiotherapy provide crucial anatomy information for patient setup and plan evaluation. Longitudinal CBCT image registration could quantify the inter-fractional anatomic changes. The purpose of this study is to propose an unsupervised deep learning based CBCT-CBCT deformable image registration. The proposed deformable registration workflow consists of training and inference stages that share the same feed-forward path through a spatial transformation-based network (STN). The STN consists of a global generative adversarial network (GlobalGAN) and a local GAN (LocalGAN) to predict the coarse- and fine-scale motions, respectively. The network was trained by minimizing the image similarity loss and the deformable vector field (DVF) regularization loss without the supervision of ground truth DVFs. During the inference stage, patches of local DVF were predicted by the trained LocalGAN and fused to form a whole-image DVF. The local whole-image DVF was subsequently combined with the GlobalGAN generated DVF to obtain final DVF. The proposed method was evaluated using 100 fractional CBCTs from 20 abdominal cancer patients in the experiments and 105 fractional CBCTs from a cohort of 21 different abdominal cancer patients in a holdout test. Qualitatively, the registration results show great alignment between the deformed CBCT images and the target CBCT image. Quantitatively, the average target registration error (TRE) calculated on the fiducial markers and manually identified landmarks was 1.91+-1.11 mm. The average mean absolute error (MAE), normalized cross correlation (NCC) between the deformed CBCT and target CBCT were 33.42+-7.48 HU, 0.94+-0.04, respectively. This promising registration method could provide fast and accurate longitudinal CBCT alignment to facilitate inter-fractional anatomic changes analysis and prediction.

Yupei Zhang, Xianjin Dai, Zhen Tian et al.

This study proposed a deep learning-based tracking method for ultrasound (US) image-guided radiation therapy. The proposed cascade deep learning model is composed of an attention network, a mask region-based convolutional neural network (mask R-CNN), and a long short-term memory (LSTM) network. The attention network learns a mapping from a US image to a suspected area of landmark motion in order to reduce the search region. The mask R-CNN then produces multiple region-of-interest (ROI) proposals in the reduced region and identifies the proposed landmark via three network heads: bounding box regression, proposal classification, and landmark segmentation. The LSTM network models the temporal relationship among the successive image frames for bounding box regression and proposal classification. To consolidate the final proposal, a selection method is designed according to the similarities between sequential frames. The proposed method was tested on the liver US tracking datasets used in the Medical Image Computing and Computer Assisted Interventions (MICCAI) 2015 challenges, where the landmarks were annotated by three experienced observers to obtain their mean positions. Five-fold cross-validation on the 24 given US sequences with ground truths shows that the mean tracking error for all landmarks is 0.65+/-0.56 mm, and the errors of all landmarks are within 2 mm. We further tested the proposed model on 69 landmarks from the testing dataset that has a similar image pattern to the training pattern, resulting in a mean tracking error of 0.94+/-0.83 mm. Our experimental results have demonstrated the feasibility and accuracy of our proposed method in tracking liver anatomic landmarks using US images, providing a potential solution for real-time liver tracking for active motion management during radiation therapy.

Yang Lei, Luke A. Matkovic, Justin Roper et al.

This paper aims to create a deep learning framework that can estimate the deformation vector field (DVF) for directly registering abdominal MRI-CT images. The proposed method assumed a diffeomorphic deformation. By using topology-preserved deformation features extracted from the probabilistic diffeomorphic registration model, abdominal motion can be accurately obtained and utilized for DVF estimation. The model integrated Swin transformers, which have demonstrated superior performance in motion tracking, into the convolutional neural network (CNN) for deformation feature extraction. The model was optimized using a cross-modality image similarity loss and a surface matching loss. To compute the image loss, a modality-independent neighborhood descriptor (MIND) was used between the deformed MRI and CT images. The surface matching loss was determined by measuring the distance between the warped coordinates of the surfaces of contoured structures on the MRI and CT images. The deformed MRI image was assessed against the CT image using the target registration error (TRE), Dice similarity coefficient (DSC), and mean surface distance (MSD) between the deformed contours of the MRI image and manual contours of the CT image. When compared to only rigid registration, DIR with the proposed method resulted in an increase of the mean DSC values of the liver and portal vein from 0.850 and 0.628 to 0.903 and 0.763, a decrease of the mean MSD of the liver from 7.216 mm to 3.232 mm, and a decrease of the TRE from 26.238 mm to 8.492 mm. The proposed deformable image registration method based on a diffeomorphic transformer provides an effective and efficient way to generate an accurate DVF from an MRI-CT image pair of the abdomen. It could be utilized in the current treatment planning workflow for liver radiotherapy.

Yang Lei, Yabo Fu, Tonghe Wang et al.

This paper presents a review of deep learning (DL) in multi-organ segmentation. We summarized the latest DL-based methods for medical image segmentation and applications. These methods were classified into six categories according to their network design. For each category, we listed the surveyed works, highlighted important contributions and identified specific challenges. Following the detailed review of each category, we briefly discussed its achievements, shortcomings and future potentials. We provided a comprehensive comparison among DL-based methods for thoracic and head & neck multiorgan segmentation using benchmark datasets, including the 2017 AAPM Thoracic Auto-segmentation Challenge datasets and 2015 MICCAI Head Neck Auto-Segmentation Challenge datasets.

Tonghe Wang, Yang Lei, Yabo Fu et al.

This paper reviewed the machine learning-based studies for quantitative positron emission tomography (PET). Specifically, we summarized the recent developments of machine learning-based methods in PET attenuation correction and low-count PET reconstruction by listing and comparing the proposed methods, study designs and reported performances of the current published studies with brief discussion on representative studies. The contributions and challenges among the reviewed studies were summarized and highlighted in the discussion part followed by.

Yabo Fu, Yang Lei, Tonghe Wang et al.

This paper presents a review of deep learning (DL) based medical image registration methods. We summarized the latest developments and applications of DL-based registration methods in the medical field. These methods were classified into seven categories according to their methods, functions and popularity. A detailed review of each category was presented, highlighting important contributions and identifying specific challenges. A short assessment was presented following the detailed review of each category to summarize its achievements and future potentials. We provided a comprehensive comparison among DL-based methods for lung and brain deformable registration using benchmark datasets. Lastly, we analyzed the statistics of all the cited works from various aspects, revealing the popularity and future trend of development in medical image registration using deep learning.