Fiber Orientation Estimation Guided by a Deep Network

Diffusion magnetic resonance imaging (dMRI) is currently the only tool for noninvasively imaging the brain's white matter tracts. The fiber orientation (FO) is a key feature computed from dMRI for fiber tract reconstruction. Because the number of FOs in a voxel is usually small, dictionary-based sparse reconstruction has been used to estimate FOs with a relatively small number of diffusion gradients. However, accurate FO estimation in regions with complex FO configurations in the presence of noise can still be challenging. In this work we explore the use of a deep network for FO estimation in a dictionary-based framework and propose an algorithm named Fiber Orientation Reconstruction guided by a Deep Network (FORDN). FORDN consists of two steps. First, we use a smaller dictionary encoding coarse basis FOs to represent the diffusion signals. To estimate the mixture fractions of the dictionary atoms (and thus coarse FOs), a deep network is designed specifically for solving the sparse reconstruction problem. Here, the smaller dictionary is used to reduce the computational cost of training. Second, the coarse FOs inform the final FO estimation, where a larger dictionary encoding dense basis FOs is used and a weighted l1-norm regularized least squares problem is solved to encourage FOs that are consistent with the network output. FORDN was evaluated and compared with state-of-the-art algorithms that estimate FOs using sparse reconstruction on simulated and real dMRI data, and the results demonstrate the benefit of using a deep network for FO estimation.Comment: A shorter version is accepted by MICCAI 201

A transversal approach for patch-based label fusion via matrix completion

Recently, multi-atlas patch-based label fusion has received an increasing interest in the medical image segmentation field. After warping the anatomical labels from the atlas images to the target image by registration, label fusion is the key step to determine the latent label for each target image point. Two popular types of patch-based label fusion approaches are (1) reconstruction-based approaches that compute the target labels as a weighted average of atlas labels, where the weights are derived by reconstructing the target image patch using the atlas image patches; and (2) classification-based approaches that determine the target label as a mapping of the target image patch, where the mapping function is often learned using the atlas image patches and their corresponding labels. Both approaches have their advantages and limitations. In this paper, we propose a novel patch-based label fusion method to combine the above two types of approaches via matrix completion (and hence, we call it transversal). As we will show, our method overcomes the individual limitations of both reconstruction-based and classification-based approaches. Since the labeling confidences may vary across the target image points, we further propose a sequential labeling framework that first labels the highly confident points and then gradually labels more challenging points in an iterative manner, guided by the label information determined in the previous iterations. We demonstrate the performance of our novel label fusion method in segmenting the hippocampus in the ADNI dataset, subcortical and limbic structures in the LONI dataset, and mid-brain structures in the SATA dataset. We achieve more accurate segmentation results than both reconstruction-based and classification-based approaches. Our label fusion method is also ranked 1st in the online SATA Multi-Atlas Segmentation Challenge

An Iterative Co-Saliency Framework for RGBD Images

As a newly emerging and significant topic in computer vision community, co-saliency detection aims at discovering the common salient objects in multiple related images. The existing methods often generate the co-saliency map through a direct forward pipeline which is based on the designed cues or initialization, but lack the refinement-cycle scheme. Moreover, they mainly focus on RGB image and ignore the depth information for RGBD images. In this paper, we propose an iterative RGBD co-saliency framework, which utilizes the existing single saliency maps as the initialization, and generates the final RGBD cosaliency map by using a refinement-cycle model. Three schemes are employed in the proposed RGBD co-saliency framework, which include the addition scheme, deletion scheme, and iteration scheme. The addition scheme is used to highlight the salient regions based on intra-image depth propagation and saliency propagation, while the deletion scheme filters the saliency regions and removes the non-common salient regions based on interimage constraint. The iteration scheme is proposed to obtain more homogeneous and consistent co-saliency map. Furthermore, a novel descriptor, named depth shape prior, is proposed in the addition scheme to introduce the depth information to enhance identification of co-salient objects. The proposed method can effectively exploit any existing 2D saliency model to work well in RGBD co-saliency scenarios. The experiments on two RGBD cosaliency datasets demonstrate the effectiveness of our proposed framework.Comment: 13 pages, 13 figures, Accepted by IEEE Transactions on Cybernetics 2017. Project URL: https://rmcong.github.io/proj_RGBD_cosal_tcyb.htm