arXiv subjects

Chuyang Ye

Publications and source records attributed to Chuyang Ye.

27 records · Page 2Linked to original sources

arXiv2021

Knowledge Transfer for Few-shot Segmentation of Novel White Matter Tracts

Convolutional neural networks (CNNs) have achieved stateof-the-art performance for white matter (WM) tract segmentation based on diffusion magnetic resonance imaging (dMRI). These CNNs require a large number of manual delineations of the WM tracts of interest for training, which are generally labor-intensive and costly. The expensive manual delineation can be a particular disadvantage when novel WM tracts, i.e., tracts that have not been included in existing manual delineations, are to be analyzed. To accurately segment novel WM tracts, it is desirable to transfer the knowledge learned about existing WM tracts, so that even with only a few delineations of the novel WM tracts, CNNs can learn adequately for the segmentation. In this paper, we explore the transfer of such knowledge to the segmentation of novel WM tracts in the few-shot setting. Although a classic fine-tuning strategy can be used for the purpose, the information in the last task-specific layer for segmenting existing WM tracts is completely discarded. We hypothesize that the weights of this last layer can bear valuable information for segmenting the novel WM tracts and thus completely discarding the information is not optimal. In particular, we assume that the novel WM tracts can correlate with existing WM tracts and the segmentation of novel WM tracts can be predicted with the logits of existing WM tracts. In this way, better initialization of the last layer than random initialization can be achieved for fine-tuning. Further, we show that a more adaptive use of the knowledge in the last layer for segmenting existing WM tracts can be conveniently achieved by simply inserting a warmup stage before classic fine-tuning. The proposed method was evaluated on a publicly available dMRI dataset, where we demonstrate the benefit of our method for few-shot segmentation of novel WM tracts.

cs.CV↗

arXiv2020

Segmentation-based Method combined with Dynamic Programming for Brain Midline Delineation

The midline related pathological image features are crucial for evaluating the severity of brain compression caused by stroke or traumatic brain injury (TBI). The automated midline delineation not only improves the assessment and clinical decision making for patients with stroke symptoms or head trauma but also reduces the time of diagnosis. Nevertheless, most of the previous methods model the midline by localizing the anatomical points, which are hard to detect or even missing in severe cases. In this paper, we formulate the brain midline delineation as a segmentation task and propose a three-stage framework. The proposed framework firstly aligns an input CT image into the standard space. Then, the aligned image is processed by a midline detection network (MD-Net) integrated with the CoordConv Layer and Cascade AtrousCconv Module to obtain the probability map. Finally, we formulate the optimal midline selection as a pathfinding problem to solve the problem of the discontinuity of midline delineation. Experimental results show that our proposed framework can achieve superior performance on one in-house dataset and one public dataset.

eess.IV↗

arXiv2019

Knowledge Transfer between Datasets for Learning-based Tissue Microstructure Estimation

Learning-based approaches, especially those based on deep networks, have enabled high-quality estimation of tissue microstructure from low-quality diffusion magnetic resonance imaging (dMRI) scans, which are acquired with a limited number of diffusion gradients and a relatively poor spatial resolution. These learning-based approaches to tissue microstructure estimation require acquisitions of training dMRI scans with high-quality diffusion signals, which are densely sampled in the q-space and have a high spatial resolution. However, the acquisition of training scans may not be available for all datasets. Therefore, we explore knowledge transfer between different dMRI datasets so that learning-based tissue microstructure estimation can be applied for datasets where training scans are not acquired. Specifically, for a target dataset of interest, where only low-quality diffusion signals are acquired without training scans, we exploit the information in a source dMRI dataset acquired with high-quality diffusion signals. We interpolate the diffusion signals in the source dataset in the q-space using a dictionary-based signal representation, so that the interpolated signals match the acquisition scheme of the target dataset. Then, the interpolated signals are used together with the high-quality tissue microstructure computed from the source dataset to train deep networks that perform tissue microstructure estimation for the target dataset. Experiments were performed on brain dMRI scans with low-quality diffusion signals, where the benefit of the proposed strategy is demonstrated.

eess.IV↗

arXiv2019

Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model

Automated brain lesion segmentation provides valuable information for the analysis and intervention of patients. In particular, methods based on convolutional neural networks (CNNs) have achieved state-of-the-art segmentation performance. However, CNNs usually require a decent amount of annotated data, which may be costly and time-consuming to obtain. Since unannotated data is generally abundant, it is desirable to use unannotated data to improve the segmentation performance for CNNs when limited annotated data is available. In this work, we propose a semi-supervised learning (SSL) approach to brain lesion segmentation, where unannotated data is incorporated into the training of CNNs. We adapt the mean teacher model, which is originally developed for SSL-based image classification, for brain lesion segmentation. Assuming that the network should produce consistent outputs for similar inputs, a loss of segmentation consistency is designed and integrated into a self-ensembling framework. Specifically, we build a student model and a teacher model, which share the same CNN architecture for segmentation. The student and teacher models are updated alternately. At each step, the student model learns from the teacher model by minimizing the weighted sum of the segmentation loss computed from annotated data and the segmentation consistency loss between the teacher and student models computed from unannotated data. Then, the teacher model is updated by combining the updated student model with the historical information of teacher models using an exponential moving average strategy. For demonstration, the proposed approach was evaluated on ischemic stroke lesion segmentation, where it improves stroke lesion segmentation with the incorporation of unannotated data.

cs.CV↗

arXiv2018

Subdivisions of the posteromedial cortex in disorders of consciousness

Evidence suggests that disruptions of the posteromedial cortex (PMC) and posteromedial corticothalamic connectivity contribute to disorders of consciousness (DOCs). While most previous studies treated the PMC as a whole, this structure is functionally heterogeneous. The present study investigated whether particular subdivisions of the PMC are specifically associated with DOCs. Participants were DOC patients, 21 vegetative state/unresponsive wakefulness syndrome (VS/UWS), 12 minimally conscious state (MCS), and 29 healthy controls. Individual PMC and thalamus were divided into distinct subdivisions by their fiber tractograpy to each other and default mode regions, and white matter integrity and brain activity between/within subdivisions were assessed. The thalamus was represented mainly in the dorsal and posterior portions of the PMC, and the white matter tracts connecting these subdivisions to the thalamus had less integrity in VS/UWS patients than in MCS patients and healthy controls, as well as in patients who did not recover after 12 months than in patients who did. The structural substrates were validated by finding impaired functional fluctuations within this PMC subdivision. This study is the first to show that tracts from dorsal and posterior subdivisions of the PMC to the thalamus contribute to DOCs.

q-bio.NC↗

arXiv2017

Learning-based Ensemble Average Propagator Estimation

By capturing the anisotropic water diffusion in tissue, diffusion magnetic resonance imaging (dMRI) provides a unique tool for noninvasively probing the tissue microstructure and orientation in the human brain. The diffusion profile can be described by the ensemble average propagator (EAP), which is inferred from observed diffusion signals. However, accurate EAP estimation using the number of diffusion gradients that is clinically practical can be challenging. In this work, we propose a deep learning algorithm for EAP estimation, which is named learning-based ensemble average propagator estimation (LEAPE). The EAP is commonly represented by a basis and its associated coefficients, and here we choose the SHORE basis and design a deep network to estimate the coefficients. The network comprises two cascaded components. The first component is a multiple layer perceptron (MLP) that simultaneously predicts the unknown coefficients. However, typical training loss functions, such as mean squared errors, may not properly represent the geometry of the possibly non-Euclidean space of the coefficients, which in particular causes problems for the extraction of directional information from the EAP. Therefore, to regularize the training, in the second component we compute an auxiliary output of approximated fiber orientation (FO) errors with the aid of a second MLP that is trained separately. We performed experiments using dMRI data that resemble clinically achievable $q$-space sampling, and observed promising results compared with the conventional EAP estimation method.

cs.CV↗

arXiv2017

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.

cs.CV↗

arXiv2017

Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework

Diffusion magnetic resonance imaging (dMRI) provides a unique tool for noninvasively probing the microstructure of the neuronal tissue. The NODDI model has been a popular approach to the estimation of tissue microstructure in many neuroscience studies. It represents the diffusion signals with three types of diffusion in tissue: intra-cellular, extra-cellular, and cerebrospinal fluid compartments. However, the original NODDI method uses a computationally expensive procedure to fit the model and could require a large number of diffusion gradients for accurate microstructure estimation, which may be impractical for clinical use. Therefore, efforts have been devoted to efficient and accurate NODDI microstructure estimation with a reduced number of diffusion gradients. In this work, we propose a deep network based approach to the NODDI microstructure estimation, which is named Microstructure Estimation using a Deep Network (MEDN). Motivated by the AMICO algorithm which accelerates the computation of NODDI parameters, we formulate the microstructure estimation problem in a dictionary-based framework. The proposed network comprises two cascaded stages. The first stage resembles the solution to a dictionary-based sparse reconstruction problem and the second stage computes the final microstructure using the output of the first stage. The weights in the two stages are jointly learned from training data, which is obtained from training dMRI scans with diffusion gradients that densely sample the q-space. The proposed method was applied to brain dMRI scans, where two shells each with 30 gradient directions (60 diffusion gradients in total) were used. Estimation accuracy with respect to the gold standard was measured and the results demonstrate that MEDN outperforms the competing algorithms.

cs.CV↗

arXiv2016

Estimation of Fiber Orientations Using Neighborhood Information

Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted l1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.

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