arXiv subjects

Dinggang Shen

Publications and source records attributed to Dinggang Shen.

At least 163 records · Page 9Linked to original sources

arXiv2019

Brain Network Construction and Classification Toolbox (BrainNetClass)

Brain functional network has become an increasingly used approach in understanding brain functions and diseases. Many network construction methods have been developed, whereas the majority of the studies still used static pairwise Pearson's correlation-based functional connectivity. The goal of this work is to introduce a toolbox namely "Brain Network Construction and Classification" (BrainNetClass) to the field to promote more advanced brain network construction methods. It comprises various brain network construction methods, including some state-of-the-art methods that were recently developed to capture more complex interactions among brain regions along with connectome feature extraction, reduction, parameter optimization towards network-based individualized classification. BrainNetClass is a MATLAB-based, open-source, cross-platform toolbox with graphical user-friendly interfaces for cognitive and clinical neuroscientists to perform rigorous computer-aided diagnosis with interpretable result presentations even though they do not possess neuroimage computing and machine learning knowledge. We demonstrate the implementations of this toolbox on real resting-state functional MRI datasets. BrainNetClass (v1.0) can be downloaded from https://github.com/zzstefan/BrainNetClass.

q-bio.NC↗

arXiv2019

Semantic-guided Encoder Feature Learning for Blurry Boundary Delineation

Encoder-decoder architectures are widely adopted for medical image segmentation tasks. With the lateral skip connection, the models can obtain and fuse both semantic and resolution information in deep layers to achieve more accurate segmentation performance. However, in many applications (e.g., blurry boundary images), these models often cannot precisely locate complex boundaries and segment tiny isolated parts. To solve this challenging problem, we firstly analyze why simple skip connections are not enough to help accurately locate indistinct boundaries and argue that it is due to the fuzzy information in the skip connection provided in the encoder layers. Then we propose a semantic-guided encoder feature learning strategy to learn both high resolution and rich semantic encoder features so that we can more accurately locate the blurry boundaries, which can also enhance the network by selectively learning discriminative features. Besides, we further propose a soft contour constraint mechanism to model the blurry boundary detection. Experimental results on real clinical datasets show that our proposed method can achieve state-of-the-art segmentation accuracy, especially for the blurry regions. Further analysis also indicates that our proposed network components indeed contribute to the improvement of performance. Experiments on additional datasets validate the generalization ability of our proposed method.

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arXiv2019

Mitigating Gyral Bias in Cortical Tractography via Asymmetric Fiber Orientation Distributions

Diffusion tractography in brain connectomics often involves tracing axonal trajectories across gray-white matter boundaries in gyral blades of complex cortical convolutions. To date, gyral bias is observed in most tractography algorithms with streamlines predominantly terminating at gyral crowns instead of sulcal banks. This work demonstrates that asymmetric fiber orientation distribution functions (AFODFs), computed via a multi-tissue global estimation framework, can mitigate the effects of gyral bias, enabling fiber streamlines at gyral blades to make sharper turns into the cortical gray matter. We use ex-vivo data of an adult rhesus macaque and in-vivo data from the Human Connectome Project (HCP) to show that the fiber streamlines given by AFODFs bend more naturally into the cortex than the conventional symmetric FODFs in typical gyral blades. We demonstrate that AFODF tractography improves cortico-cortical connectivity and provides highly consistent outcomes between two different field strengths (3T and 7T).

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arXiv2019

FRNET: Flattened Residual Network for Infant MRI Skull Stripping

Skull stripping for brain MR images is a basic segmentation task. Although many methods have been proposed, most of them focused mainly on the adult MR images. Skull stripping for infant MR images is more challenging due to the small size and dynamic intensity changes of brain tissues during the early ages. In this paper, we propose a novel CNN based framework to robustly extract brain region from infant MR image without any human assistance. Specifically, we propose a simplified but more robust flattened residual network architecture (FRnet). We also introduce a new boundary loss function to highlight ambiguous and low contrast regions between brain and non-brain regions. To make the whole framework more robust to MR images with different imaging quality, we further introduce an artifact simulator for data augmentation. We have trained and tested our proposed framework on a large dataset (N=343), covering newborns to 48-month-olds, and obtained performance better than the state-of-the-art methods in all age groups.

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arXiv2019

Spherical U-Net on Cortical Surfaces: Methods and Applications

Convolutional Neural Networks (CNNs) have been providing the state-of-the-art performance for learning-related problems involving 2D/3D images in Euclidean space. However, unlike in the Euclidean space, the shapes of many structures in medical imaging have a spherical topology in a manifold space, e.g., brain cortical or subcortical surfaces represented by triangular meshes, with large inter-subject and intrasubject variations in vertex number and local connectivity. Hence, there is no consistent neighborhood definition and thus no straightforward convolution/transposed convolution operations for cortical/subcortical surface data. In this paper, by leveraging the regular and consistent geometric structure of the resampled cortical surface mapped onto the spherical space, we propose a novel convolution filter analogous to the standard convolution on the image grid. Accordingly, we develop corresponding operations for convolution, pooling, and transposed convolution for spherical surface data and thus construct spherical CNNs. Specifically, we propose the Spherical U-Net architecture by replacing all operations in the standard U-Net with their spherical operation counterparts. We then apply the Spherical U-Net to two challenging and neuroscientifically important tasks in infant brains: cortical surface parcellation and cortical attribute map development prediction. Both applications demonstrate the competitive performance in the accuracy, computational efficiency, and effectiveness of our proposed Spherical U-Net, in comparison with the state-of-the-art methods.

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arXiv2019

Deep Morphological Simplification Network (MS-Net) for Guided Registration of Brain Magnetic Resonance Images

Objective: Deformable brain MR image registration is challenging due to large inter-subject anatomical variation. For example, the highly complex cortical folding pattern makes it hard to accurately align corresponding cortical structures of individual images. In this paper, we propose a novel deep learning way to simplify the difficult registration problem of brain MR images. Methods: We train a morphological simplification network (MS-Net), which can generate a "simple" image with less anatomical details based on the "complex" input. With MS-Net, the complexity of the fixed image or the moving image under registration can be reduced gradually, thus building an individual (simplification) trajectory represented by MS-Net outputs. Since the generated images at the ends of the two trajectories (of the fixed and moving images) are so simple and very similar in appearance, they are easy to register. Thus, the two trajectories can act as a bridge to link the fixed and the moving images, and guide their registration. Results: Our experiments show that the proposed method can achieve highly accurate registration performance on different datasets (i.e., NIREP, LPBA, IBSR, CUMC, and MGH). Moreover, the method can be also easily transferred across diverse image datasets and obtain superior accuracy on surface alignment. Conclusion and Significance: We propose MS-Net as a powerful and flexible tool to simplify brain MR images and their registration. To our knowledge, this is the first work to simplify brain MR image registration by deep learning, instead of estimating deformation field directly.

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arXiv2018

Deep Chronnectome Learning via Full Bidirectional Long Short-Term Memory Networks for MCI Diagnosis

Brain functional connectivity (FC) extracted from resting-state fMRI (RS-fMRI) has become a popular approach for disease diagnosis, where discriminating subjects with mild cognitive impairment (MCI) from normal controls (NC) is still one of the most challenging problems. Dynamic functional connectivity (dFC), consisting of time-varying spatiotemporal dynamics, may characterize "chronnectome" diagnostic information for improving MCI classification. However, most of the current dFC studies are based on detecting discrete major brain status via spatial clustering, which ignores rich spatiotemporal dynamics contained in such chronnectome. We propose Deep Chronnectome Learning for exhaustively mining the comprehensive information, especially the hidden higher-level features, i.e., the dFC time series that may add critical diagnostic power for MCI classification. To this end, we devise a new Fully-connected Bidirectional Long Short-Term Memory Network (Full-BiLSTM) to effectively learn the periodic brain status changes using both past and future information for each brief time segment and then fuse them to form the final output. We have applied our method to a rigorously built large-scale multi-site database (i.e., with 164 data from NCs and 330 from MCIs, which can be further augmented by 25 folds). Our method outperforms other state-of-the-art approaches with an accuracy of 73.6% under solid cross-validations. We also made extensive comparisons among multiple variants of LSTM models. The results suggest high feasibility of our method with promising value also for other brain disorder diagnoses.

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arXiv2018

Noise Reduction in Diffusion MRI Using Non-Local Self-Similar Information in Joint x-q Space

Diffusion MRI affords valuable insights into white matter microstructures, but suffers from low signal-to-noise ratio (SNR), especially at high diffusion weighting (i.e., b-value). To avoid time-intensive repeated acquisition, post-processing algorithms are often used to reduce noise. Among existing methods, non-local means (NLM) has been shown to be particularly effective. However, most NLM algorithms for diffusion MRI focus on patch matching in the spatial domain (i.e., x-space) and disregard the fact that the data live in a combined 6D space covering both spatial domain and diffusion wavevector domain (i.e., q-space). This drawback leads to inaccurate patch matching in curved white matter structures and hence the inability to effectively use recurrent information for noise reduction. The goal of this paper is to overcome this limitation by extending NLM to the joint x-q space. Specifically, we define for each point in the x-q space a spherical patch from which we extract rotation-invariant features for patch matching. The ability to perform patch matching across q-samples allows patches from differentially orientated structures to be used for effective noise removal. Extensive experiments on synthetic, repeated acquisition, and real data demonstrate that our method outperforms state-of-the-art methods, both qualitatively and quantitatively.

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arXiv2018

Angular Upsampling in Infant Diffusion MRI Using Neighborhood Matching in x-q Space

Diffusion MRI requires sufficient coverage of the diffusion wavevector space, also known as the q-space, to adequately capture the pattern of water diffusion in various directions and scales. As a result, the acquisition time can be prohibitive for individuals who are unable to stay still in the scanner for an extensive period of time, such as infants. To address this problem, in this paper we harness non-local self-similar information in the x-q space of diffusion MRI data for q-space upsampling. Specifically, we first perform neighborhood matching to establish the relationships of signals in x-q space. The signal relationships are then used to regularize an ill-posed inverse problem related to the estimation of high angular resolution diffusion MRI data from its low-resolution counterpart. Our framework allows information from curved white matter structures to be used for effective regularization of the otherwise ill-posed problem. Extensive evaluations using synthetic and infant diffusion MRI data demonstrate the effectiveness of our method. Compared with the widely adopted interpolation methods using spherical radial basis functions and spherical harmonics, our method is able to produce high angular resolution diffusion MRI data with greater quality, both qualitatively and quantitatively.

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arXiv2018

Robust Group Comparison Using Non-Parametric Block-Based Statistics

Voxel-based analysis methods localize brain structural differences by performing voxel-wise statistical comparisons on two groups of images aligned to a common space. This procedure requires highly accurate registration as well as a sufficiently large dataset. However, in practice, the registration algorithms are not perfect due to noise, artifacts, and complex structural variations. The sample size is also limited due to low disease prevalence, recruitment difficulties, and demographic matching issues. To address these issues, in this paper, we propose a method, called block-based statistic (BBS), for robust group comparison. BBS consists of two major components: Block matching and permutation test. Specifically, based on two group of images aligned to a common space, we first perform block matching so that structural misalignments can be corrected. Then, based on results given by block matching, we conduct robust non-parametric statistical inference based on permutation test. Extensive experiments were performed on synthetic data and the real diffusion MR data of mild cognitive impairment patients. The experimental results indicate that BBS significantly improves statistical power, notwithstanding the small sample size.

stat.AP↗

arXiv2018

Interactive Medical Image Segmentation via Point-Based Interaction and Sequential Patch Learning

Due to low tissue contrast, irregular object appearance, and unpredictable location variation, segmenting the objects from different medical imaging modalities (e.g., CT, MR) is considered as an important yet challenging task. In this paper, we present a novel method for interactive medical image segmentation with the following merits. (1) Our design is fundamentally different from previous pure patch-based and image-based segmentation methods. We observe that during delineation, the physician repeatedly check the inside-outside intensity changing to determine the boundary, which indicates that comparison in an inside-outside manner is extremely important. Thus, we innovatively model our segmentation task as learning the representation of the bi-directional sequential patches, starting from (or ending in) the given central point of the object. This can be realized by our proposed ConvRNN network embedded with a gated memory propagation unit. (2) Unlike previous interactive methods (requiring bounding box or seed points), we only ask the physician to merely click on the rough central point of the object before segmentation, which could simultaneously enhance the performance and reduce the segmentation time. (3) We utilize our method in a multi-level framework for better performance. We systematically evaluate our method in three different segmentation tasks including CT kidney tumor, MR prostate, and PROMISE12 challenge, showing promising results compared with state-of-the-art methods. The code is available here: \href{https://github.com/sunalbert/Sequential-patch-based-segmentation}{Sequential-patch-based-segmentation}.

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arXiv2018

Deep Learning based Inter-Modality Image Registration Supervised by Intra-Modality Similarity

Non-rigid inter-modality registration can facilitate accurate information fusion from different modalities, but it is challenging due to the very different image appearances across modalities. In this paper, we propose to train a non-rigid inter-modality image registration network, which can directly predict the transformation field from the input multimodal images, such as CT and MR images. In particular, the training of our inter-modality registration network is supervised by intra-modality similarity metric based on the available paired data, which is derived from a pre-aligned CT and MR dataset. Specifically, in the training stage, to register the input CT and MR images, their similarity is evaluated on the warped MR image and the MR image that is paired with the input CT. So that, the intra-modality similarity metric can be directly applied to measure whether the input CT and MR images are well registered. Moreover, we use the idea of dual-modality fashion, in which we measure the similarity on both CT modality and MR modality. In this way, the complementary anatomies in both modalities can be jointly considered to more accurately train the inter-modality registration network. In the testing stage, the trained inter-modality registration network can be directly applied to register the new multimodal images without any paired data. Experimental results have shown that, the proposed method can achieve promising accuracy and efficiency for the challenging non-rigid inter-modality registration task and also outperforms the state-of-the-art approaches.

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arXiv2018

BIRNet: Brain Image Registration Using Dual-Supervised Fully Convolutional Networks

In this paper, we propose a deep learning approach for image registration by predicting deformation from image appearance. Since obtaining ground-truth deformation fields for training can be challenging, we design a fully convolutional network that is subject to dual-guidance: (1) Coarse guidance using deformation fields obtained by an existing registration method; and (2) Fine guidance using image similarity. The latter guidance helps avoid overly relying on the supervision from the training deformation fields, which could be inaccurate. For effective training, we further improve the deep convolutional network with gap filling, hierarchical loss, and multi-source strategies. Experiments on a variety of datasets show promising registration accuracy and efficiency compared with state-of-the-art methods.

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arXiv2017

Deep CNN ensembles and suggestive annotations for infant brain MRI segmentation

Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for 6-month infant brain, due to the poor image quality, among other difficulties inherent to infant brain MRI, e.g., the isointense contrast between white and gray matter and the severe partial volume effect due to small brain sizes. This study investigates the problem with an ensemble of semi-dense fully convolutional neural networks (CNNs), which employs T1-weighted and T2-weighted MR images as input. We demonstrate that the ensemble agreement is highly correlated with the segmentation errors. Therefore, our method provides measures that can guide local user corrections. To the best of our knowledge, this work is the first ensemble of 3D CNNs for suggesting annotations within images. Furthermore, inspired by the very recent success of dense networks, we propose a novel architecture, SemiDenseNet, which connects all convolutional layers directly to the end of the network. Our architecture allows the efficient propagation of gradients during training, while limiting the number of parameters, requiring one order of magnitude less parameters than popular medical image segmentation networks such as 3D U-Net. Another contribution of our work is the study of the impact that early or late fusions of multiple image modalities might have on the performances of deep architectures. We report evaluations of our method on the public data of the MICCAI iSEG-2017 Challenge on 6-month infant brain MRI segmentation, and show very competitive results among 21 teams, ranking first or second in most metrics.

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arXiv2017

Deep Embedding Convolutional Neural Network for Synthesizing CT Image from T1-Weighted MR Image

Recently, more and more attention is drawn to the field of medical image synthesis across modalities. Among them, the synthesis of computed tomography (CT) image from T1-weighted magnetic resonance (MR) image is of great importance, although the mapping between them is highly complex due to large gaps of appearances of the two modalities. In this work, we aim to tackle this MR-to-CT synthesis by a novel deep embedding convolutional neural network (DECNN). Specifically, we generate the feature maps from MR images, and then transform these feature maps forward through convolutional layers in the network. We can further compute a tentative CT synthesis from the midway of the flow of feature maps, and then embed this tentative CT synthesis back to the feature maps. This embedding operation results in better feature maps, which are further transformed forward in DECNN. After repeat-ing this embedding procedure for several times in the network, we can eventually synthesize a final CT image in the end of the DECNN. We have validated our proposed method on both brain and prostate datasets, by also compar-ing with the state-of-the-art methods. Experimental results suggest that our DECNN (with repeated embedding op-erations) demonstrates its superior performances, in terms of both the perceptive quality of the synthesized CT image and the run-time cost for synthesizing a CT image.

cs.CV↗

arXiv2017

Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes

In diffusion MRI (dMRI), a good sampling scheme is important for efficient acquisition and robust reconstruction. Diffusion weighted signal is normally acquired on single or multiple shells in q-space. Signal samples are typically distributed uniformly on different shells to make them invariant to the orientation of structures within tissue, or the laboratory coordinate frame. The Electrostatic Energy Minimization (EEM) method, originally proposed for single shell sampling scheme in dMRI, was recently generalized to multi-shell schemes, called Generalized EEM (GEEM). GEEM has been successfully used in the Human Connectome Project (HCP). However, EEM does not directly address the goal of optimal sampling, i.e., achieving large angular separation between sampling points. In this paper, we propose a more natural formulation, called Spherical Code (SC), to directly maximize the minimal angle between different samples in single or multiple shells. We consider not only continuous problems to design single or multiple shell sampling schemes, but also discrete problems to uniformly extract sub-sampled schemes from an existing single or multiple shell scheme, and to order samples in an existing scheme. We propose five algorithms to solve the above problems, including an incremental SC (ISC), a sophisticated greedy algorithm called Iterative Maximum Overlap Construction (IMOC), an 1-Opt greedy method, a Mixed Integer Linear Programming (MILP) method, and a Constrained Non-Linear Optimization (CNLO) method. To our knowledge, this is the first work to use the SC formulation for single or multiple shell sampling schemes in dMRI. Experimental results indicate that SC methods obtain larger angular separation and better rotational invariance than the state-of-the-art EEM and GEEM. The related codes and a tutorial have been released in DMRITool.

physics.med-ph↗

arXiv2016

Medical Image Synthesis with Context-Aware Generative Adversarial Networks

Computed tomography (CT) is critical for various clinical applications, e.g., radiotherapy treatment planning and also PET attenuation correction. 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 any radiations. Therefore, recently, researchers are greatly motivated to estimate CT image from its corresponding MR image of the same subject for the case of radiotherapy planning. In this paper, we propose a data-driven approach to address this challenging problem. Specifically, we train a fully convolutional network to generate CT given an MR image. To better model the nonlinear relationship from MRI to CT and to produce more realistic images, we propose to use the adversarial training strategy and an image gradient difference loss function. We further apply AutoContext Model to implement a context-aware generative adversarial network. Experimental results show that our method is accurate and robust for predicting CT images from MRI images, and also outperforms three state-of-the-art methods under comparison.

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arXiv2015

Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data

Due to its causal semantics, Bayesian networks (BN) have been widely employed to discover the underlying data relationship in exploratory studies, such as brain research. Despite its success in modeling the probability distribution of variables, BN is naturally a generative model, which is not necessarily discriminative. This may cause the ignorance of subtle but critical network changes that are of investigation values across populations. In this paper, we propose to improve the discriminative power of BN models for continuous variables from two different perspectives. This brings two general discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the first framework, we employ Fisher kernel to bridge the generative models of GBN and the discriminative classifiers of SVMs, and convert the GBN parameter learning to Fisher kernel learning via minimizing a generalization error bound of SVMs. In the second framework, we employ the max-margin criterion and build it directly upon GBN models to explicitly optimize the classification performance of the GBNs. The advantages and disadvantages of the two frameworks are discussed and experimentally compared. Both of them demonstrate strong power in learning discriminative parameters of GBNs for neuroimaging based brain network analysis, as well as maintaining reasonable representation capacity. The contributions of this paper also include a new Directed Acyclic Graph (DAG) constraint with theoretical guarantee to ensure the graph validity of GBN.

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