Computed tomography (CT) is critical for various clinical applications, e.g., radiation treatment planning and also PET attenuation correction in MRI/PET scanner. However, CT exposes radiation during acquisition, which may cause side effects to patients. Compared to CT, magnetic resonance imaging (MRI) is much safer and does not involve radiations. Therefore, recently researchers are greatly motivated to estimate CT image from its corresponding MR image of the same subject for the case of radiation planning. In this paper, we propose a data-driven approach to address this challenging problem. Specifically, we train a fully convolutional network (FCN) to generate CT given the MR image. To better model the nonlinear mapping from MRI to CT and produce more realistic images, we propose to use the adversarial training strategy to train the FCN. Moreover, we propose an image-gradient-difference based loss function to alleviate the blurriness of the generated CT. We further apply Auto-Context Model (ACM) to implement a context-aware generative adversarial network. Experimental results show that our method is accurate and robust for predicting CT images from MR images, and also outperforms three state-of-the-art methods under comparison.

Positron emission tomography (PET) is an essential technique in many clinical applications such as tumor detection and brain disorder diagnosis. In order to obtain high-quality PET images, a standard-dose radioactive tracer is needed, which inevitably causes the risk of radiation exposure damage. For reducing the patient’s exposure to radiation and maintaining the high quality of PET images, in this paper, we propose a deep learning architecture to estimate the high-quality standard-dose PET (SPET) image from the combination of the low-quality low-dose PET (LPET) image and the accompanying T1-weighted acquisition from magnetic resonance imaging (MRI). Specifically, we adapt the convolutional neural network (CNN) to account for the two channel inputs of LPET and T1, and directly learn the end-to-end mapping between the inputs and the SPET output. Then, we integrate multiple CNN modules following the auto-context strategy, such that the tentatively estimated SPET of an early CNN can be iteratively refined by subsequent CNNs. Validations on real human brain PET/MRI data show that our proposed method can provide competitive estimation quality of the PET images, compared to the state-of-the-art methods. Meanwhile, our method is highly efficient to test on a new subject, e.g., spending ~2 seconds for estimating an entire SPET image in contrast to ~16 minutes by the state-of-the-art method. The results above demonstrate the potential of our method in real clinical applications.

Feature selection is a critical step in deformable image registration. In particular, selecting the most discriminative features that accurately and concisely describe complex morphological patterns in image patches improves correspondence detection, which in turn improves image registration accuracy. Furthermore, since more and more imaging modalities are being invented to better identify morphological changes in medical imaging data,, the development of deformable image registration method that scales well to new image modalities or new image applications with little to no human intervention would have a significant impact on the medical image analysis community. To address these concerns, a learning-based image registration framework is proposed that uses deep learning to discover compact and highly discriminative features upon observed imaging data. Specifically, the proposed feature selection method uses a convolutional stacked auto-encoder to identify intrinsic deep feature representations in image patches. Since deep learning is an unsupervised learning method, no ground truth label knowledge is required. This makes the proposed feature selection method more flexible to new imaging modalities since feature representations can be directly learned from the observed imaging data in a very short amount of time. Using the LONI and ADNI imaging datasets, image registration performance was compared to two existing state-of-the-art deformable image registration methods that use handcrafted features. To demonstrate the scalability of the proposed image registration framework image registration experiments were conducted on 7.0-tesla brain MR images. In all experiments, the results showed the new image registration framework consistently demonstrated more accurate registration results when compared to state-of-the-art.

Existing deformable registration methods require exhaustively iterative optimization, along with careful parameter tuning, to estimate the deformation field between images. Although some learning-based methods have been proposed for initiating deformation estimation, they are often template-specific and not flexible in practical use. In this paper, we propose a convolutional neural network (CNN) based regression model to directly learn the complex mapping from the input image pair (i.e., a pair of template and subject) to their corresponding deformation field. Specifically, our CNN architecture is designed in a patch-based manner to learn the complex mapping from the input patch pairs to their respective deformation field. First, the equalized active-points guided sampling strategy is introduced to facilitate accurate CNN model learning upon a limited image dataset. Then, the similarity-steered CNN architecture is designed, where we propose to add the auxiliary contextual cue, i.e., the similarity between input patches, to more directly guide the learning process. Experiments on different brain image datasets demonstrate promising registration performance based on our CNN model. Furthermore, it is found that the trained CNN model from one dataset can be successfully transferred to another dataset, although brain appearances across datasets are quite variable.

Groupwise registration has become more and more popular due to its attractiveness for unbiased analysis of population data. One of the most popular approaches for groupwise registration is to iteratively calculate the group mean image and then register all subject images towards the latest estimated group mean image. However, its performance might be undermined by the fuzzy mean image estimated in the very beginning of groupwise registration procedure, because all subject images are far from being well-aligned at that moment. In this paper, we first point out the significance of always keeping the group mean image sharp and clear throughout the entire groupwise registration procedure, which is intuitively important but has not been explored in the literature yet. To achieve this, we resort to developing the robust mean-image estimator by the adaptive weighting strategy, where the weights are adaptive across not only the individual subject images but also all spatial locations in the image domain. On the other hand, we notice that some subjects might have large anatomical variations from the group mean image, which challenges most of the state-of-the-art registration algorithms. To ensure good registration results in each iteration, we explore the manifold of subject images and build a minimal spanning tree (MST) with the group mean image as the root of the MST. Therefore, each subject image is only registered to its parent node often with similar shapes, and its overall transformation to the group mean image space is obtained by concatenating all deformations along the paths connecting itself to the root of the MST (the group mean image). As a result, all the subjects will be well aligned to the group mean image adaptively. Our method has been evaluated in both real and simulated datasets. In all experiments, our method outperforms the conventional algorithm which generally produces a fuzzy group mean image throughout the entire groupwise registration.