WO2024098379A1 - Fully automatic cardiac magnetic resonance imaging segmentation method based on dilated residual network - Google Patents

Fully automatic cardiac magnetic resonance imaging segmentation method based on dilated residual network Download PDF

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WO2024098379A1
WO2024098379A1 PCT/CN2022/131363 CN2022131363W WO2024098379A1 WO 2024098379 A1 WO2024098379 A1 WO 2024098379A1 CN 2022131363 W CN2022131363 W CN 2022131363W WO 2024098379 A1 WO2024098379 A1 WO 2024098379A1
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segmentation
image
network
magnetic resonance
segmentation network
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PCT/CN2022/131363
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Chinese (zh)
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夏泽洋
凡在
熊璟
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深圳先进技术研究院
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    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00Image analysis
    • G06T7/10Segmentation; Edge detection
    • G06T7/11Region-based segmentation

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  • the present invention relates to the field of biomedical engineering technology, and more specifically, to a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network.
  • Heart diseases seriously threaten human life.
  • CMRI cardiac magnetic resonance imaging
  • the constant beating of the heart makes it more difficult to obtain clear images, especially for patients with cardiovascular diseases, who are more likely to experience arrhythmias, difficulty holding their breath, etc.
  • Existing manual segmentation of images is not only time-consuming, but also difficult to guarantee accuracy. Therefore, it is necessary to realize automatic segmentation of the heart area to solve practical problems in the field of cardiac medicine.
  • Cardiac image segmentation refers to the division of cardiac images into multiple anatomically meaningful regions, based on which quantitative metrics such as myocardial mass, wall thickness, and the volumes of the left ventricle (LV) and right ventricle (RV) can be extracted. Therefore, it is particularly important to design an accurate and fully automatic cardiac segmentation algorithm.
  • DCNNs deep convolutional neural networks
  • the U-Net architecture is task-independent and has been applied to various biomedical segmentation tasks with only minor or substantial modifications.
  • U-Net is the backbone of most of the most effective ventricle segmentation algorithms.
  • patent application CN202210321078.8 provides a CT image heart segmentation method and system based on artificial intelligence semantic segmentation. This technology reduces the impact of noise by optimizing the category probability and achieves accurate image segmentation. However, this solution does not involve the specific segmentation of the left ventricle, right ventricle, and myocardium in the heart, and cannot obtain independent heart tissue images.
  • Patent application CN202110391121.3 describes a cardiac segmentation model and pathology classification model training, cardiac segmentation, and pathology classification method and device based on cardiac MRI. This technology can greatly suppress background interference and promote rapid convergence of neural network training, but no improvement method is proposed for image segmentation accuracy and robustness.
  • the purpose of the present invention is to overcome the defects of the prior art and provide a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network.
  • the method comprises the following steps:
  • the segmentation network is constructed based on the residual network U-Net, and the bottleneck layer of the residual network adopts a dilated convolution block with a set dilation rate to combine the encoding path and the decoding path.
  • the advantage of the present invention is that it proposes a fully automatic cardiac MRI (magnetic resonance imaging) segmentation method based on a dilated residual network, which can accurately segment the right ventricle, left ventricle, myocardium and other regions from cardiac MRI images, realize fully automatic segmentation of cardiac images, and improve the performance of cardiac region image segmentation.
  • MRI magnetic resonance imaging
  • FIG1 is a flow chart of a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network according to an embodiment of the present invention
  • FIG2 is a schematic diagram of a process from raw magnetic resonance image data to image segmentation according to an embodiment of the present invention
  • FIG3 is a diagram of an automatic image segmentation architecture based on U-Net according to an embodiment of the present invention.
  • FIG4 is a schematic diagram of the architecture of an expanded residual block according to an embodiment of the present invention.
  • FIG5 is a schematic diagram of image segmentation results for an ACDC test data set according to an embodiment of the present invention.
  • Conv-convolution Norm-regularization; Maxpool-maximum pooling; UpConv-up convolution; Deconvolution-deconvolution; Skip-connection-skip connection; Pixel-wise addition-pixel-by-pixel addition; Kernel-kernel; Concatenation-cascade; Stride-stride; End Systole-end systole; End Diastole-end diastole.
  • the present invention develops a fully automatic segmentation method for right ventricle (RV), myocardium (MYO) and left ventricle (LV) by combining short-axis CMRI (cinema magnetic resonance imaging) sequence images.
  • the method captures multi-resolution features in U-Net by dilating convolutional residual network (DRN), thereby significantly increasing spatial and temporal information and maintaining positioning accuracy.
  • DNN convolutional residual network
  • the output of each dilation path is added pixel by pixel to improve the training response.
  • the provided fully automatic cardiac magnetic resonance imaging segmentation method based on dilated residual network includes the following steps:
  • Step S110 preprocessing the data set to obtain training samples.
  • the size of a three-dimensional image is L ⁇ W ⁇ H, where L is the length of the image sequence, W is the width of the image, and H is the length of the image.
  • training samples are obtained through a data preprocessing process.
  • ACDC Advanced Conditions Dataset with Correspondences
  • images are taken as an example.
  • the input image is resampled.
  • the ACDC dataset has a voxel spacing problem. Since the convolutional neural network cannot explain the voxel spacing, all images are resampled to the same voxel spacing of 1.52 ⁇ 1.52 ⁇ 6.35mm.
  • the data preprocessing process takes into account that the voxel spacing directly affects the overall voxel size of the image, and also affects the amount of contextual information that the convolutional neural network can extract from the image patch. In addition, if the voxel spacing is greatly increased, the image size will be reduced to the point where details are lost, so it is necessary to ensure that there is a trade-off between the amount of contextual information included in the network patch size and the amount of detail retained in the image data to obtain the best performance.
  • all images are resampled to a median of 256 ⁇ 256 pixels.
  • magnetic resonance images of the ACDC dataset are obtained using multi-layer magnetic resonance movie images. For example, 2D-MRI (magnetic resonance imaging) slices of each patient and their associated annotations are extracted. And normalization is performed slice by slice for each time frame.
  • 2D-MRI magnetic resonance imaging
  • Step S120 expanding the training samples through data enhancement and constructing a training set.
  • Step S130 constructing a segmentation network based on the dilated residual network.
  • a heart segmentation network based on the U-net network is used as an example for explanation, as shown in Figures 3 and 4, where Figure 4 corresponds to the dilated residual block architecture of Figure 3.
  • the segmentation network follows the overall architecture of the encoder-decoder throughout the segmentation process.
  • a contraction path is constructed using 5 encoding blocks; each block consists of 2 convolutional layers with 3 ⁇ 3 kernels and 2 ⁇ 2 maximum pooling operations with a stride of 2. Initially, 32 convolution kernels are selected. After each maximum pooling operation, the convolution kernel will increase, resulting in 320 convolution kernels in the bottleneck layer of the U-Net.
  • the spatial dimension of the feature map is reduced by a factor of 2 through a downsampling operation.
  • the rectified linear unit (ReLU) is replaced by a leaky linear rectifier, and instance regularization is used instead of normalization (BN).
  • the encoding and decoding paths are combined at the U-Net bottleneck layer by a dilated residual network (DRN), which captures global context and recovers spatial and temporal information without affecting the resolution of the segmentation map.
  • DRN dilated residual network
  • the dilated residual network can effectively adjust the depth of the convolutional layer without degrading the network performance.
  • the dilated residual network captures contextual image information, high spatial resolution, and multi-texture features.
  • the process of the decoding path is similar to that of the encoding path, however, the order of operations is reversed.
  • the U-Net architecture provides the advantage of reusing the encoded feature maps from the encoding block to its corresponding level, where the spatial dimensions match. This can be achieved through channel-specific cascading.
  • a 1 ⁇ 1 kernel projection operation is used at the last level of the decoding path to align the output channel dimensions with the classified categories (left ventricle, myocardium, and right ventricle).
  • all extended path outputs are aggregated by upsampling and pixel-wise addition to enhance the training response.
  • the present invention adopts an expanded convolutional network to extract more spatial information to predict small and dense image features by increasing the receptive field.
  • the discrete expanded convolution is as follows:
  • k is a discrete kernel of size (2d+1) 2
  • a dilated residual network can better expand the receptive field to achieve a promising result and avoid the loss of image information at the bottleneck of U-Net.
  • Dilated convolution introduces a new parameter called "dilation rate" to the convolution layer, which defines the spacing between the values when the convolution kernel processes the data, expanding the receptive field by adding holes.
  • y ij represents the dilated convolution with input x ij , which is a convolution kernel with length M and width N, and m and n are the input variables of the dilated convolution.
  • w(i, j) is the corresponding weight, i represents the image length index, j represents the image width index, and d represents the dilation rate.
  • Step S140 training the segmentation network using the set loss function.
  • the goal of segmentation is to detect the target object and draw a contour around it.
  • the automatically segmented contour Cp (predicted) is compared with the corresponding annotated image to measure the accuracy of the proposed method.
  • the pixels surrounded by the contour are called A p and Ag .
  • loss functions There are many types of loss functions that can be used in segmentation network training, for example, Dice similarity coefficient or Hausdorff distance or other types of loss functions.
  • DSC Dice Similarity Coefficient
  • Ap represents the pixels surrounded by the predicted contour
  • Ag represents the pixels surrounded by the real contour
  • the Hausdorff distance (HD) is a symmetric distance between the predicted and actual contours and provides the spatial resolution of the MRI cine images. The lower the HD value, the better the segmentation matching performance.
  • Cp is the predicted automatically segmented contour
  • Cg is the corresponding true labeled contour
  • d(i, j) represents the distance between the ground truth and the predicted contour
  • i represents the pixel of the predicted contour
  • j represents the pixel of the ground truth contour.
  • a dual loss function including dice loss and cross entropy loss is used to train the segmentation network.
  • the cross entropy loss is defined as follows:
  • C represents the total number of categories
  • c represents the category indicator
  • W (w 1 , w 2 , w 3 ... w n ) is a series of learnable weights
  • w n is the weight matrix of the nth layer
  • X i , W) represents the probability of a predicted pixel Xi being misclassified relative to the ground truth label pixel
  • Y(c, x) represents the target label corresponding to the input x
  • the model was trained for a total of 500 iterations, where 250 images were randomly sampled from the dataset in each iteration of the training set until all the image data was exhausted.
  • slices were randomly cropped from the training images and the network was evaluated after each iteration on the validation set. For example, a multi-class variant of the dice loss was used to train the segmentation network.
  • u and v are the one-hot encoded vectors and the image segmentation label values corresponding to the class identifiers of the activation function softmax output, i represents the image length index, and k represents the image width index; c ⁇ C is the class identifier, i.e., the left ventricle, right ventricle, myocardium, and background of the heart; ⁇ is a tiny constant.
  • the learning rate lr is recalculated according to the following formula.
  • the best model is selected to evaluate the test set to ensure that the verification of RV (right ventricle), MYO (myocardium), and LV (left ventricle) achieves the highest DSC (Dice Similarity Coefficient).
  • the network provides consistent and stable performance in all folds.
  • initial_learning_rate is the initial learning rate
  • currentepoch is the current number of iterations
  • totalepoch is the total number of iterations.
  • Step S150 for the acquired target magnetic resonance image, using the trained segmentation network to identify regions such as the right ventricle, myocardium and left ventricle.
  • the optimized model parameters can be obtained. Then, using the trained segmentation network, the regions of interest such as the right ventricle, myocardium and left ventricle, as well as the complete heart contour can be accurately distinguished. Then, based on these regions, quantitative measurements can be extracted, such as myocardial mass, the volume of the left and right ventricles, etc.
  • the present invention introduces a dilated convolutional residual network and enhances the performance of the U-Net bottleneck layer to achieve fully automatic and accurate segmentation of cardiac MRI (magnetic resonance imaging) images, which solves the limitations of the U-Net bottleneck layer, significantly enhances spatial and temporal information, and improves accuracy while maintaining spatial consistency.
  • cardiac MRI magnetic resonance imaging
  • the present invention designs an extended residual network (DRN) block to replace the original bottleneck layer of U-Net, and uses a variety of loss functions to better utilize cardiac features to train the model and improve accuracy in the process of segmenting cardiac images.
  • DNN extended residual network
  • the present invention has higher computing speed and robustness, and can be applied to a variety of cardiac CMRI (cine magnetic resonance imaging) data sets.
  • the processed data is a patient's magnetic resonance image at two different magnetic intensities, and after the data is processed, the patient's complete heart contour, left and right ventricles, and myocardial contour images can be obtained simultaneously.
  • the present invention may be a system, a method and/or a computer program product.
  • the computer program product may include a computer-readable storage medium carrying computer-readable program instructions for causing a processor to implement various aspects of the present invention.
  • Computer readable storage medium can be a tangible device that can hold and store instructions used by an instruction execution device.
  • Computer readable storage medium can be, for example, but not limited to, an electrical storage device, a magnetic storage device, an optical storage device, an electromagnetic storage device, a semiconductor storage device, or any suitable combination thereof.
  • Non-exhaustive list of computer readable storage medium include: a portable computer disk, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), a static random access memory (SRAM), a portable compact disk read-only memory (CD-ROM), a digital versatile disk (DVD), a memory stick, a floppy disk, a mechanical encoding device, for example, a punch card or a convex structure in a groove on which instructions are stored, and any suitable combination thereof.
  • RAM random access memory
  • ROM read-only memory
  • EPROM or flash memory erasable programmable read-only memory
  • SRAM static random access memory
  • CD-ROM compact disk read-only memory
  • DVD digital versatile disk
  • memory stick a floppy disk
  • mechanical encoding device for example, a punch card or a convex structure in a groove on which instructions are stored, and any suitable combination thereof.
  • the computer readable storage medium used here is not interpreted as a transient signal itself, such as a radio wave or other freely propagating electromagnetic wave, an electromagnetic wave propagated by a waveguide or other transmission medium (for example, a light pulse by an optical fiber cable), or an electrical signal transmitted by a wire.
  • the computer-readable program instructions described herein can be downloaded from a computer-readable storage medium to each computing/processing device, or downloaded to an external computer or external storage device via a network, such as the Internet, a local area network, a wide area network, and/or a wireless network.
  • the network can include copper transmission cables, optical fiber transmissions, wireless transmissions, routers, firewalls, switches, gateway computers, and/or edge servers.
  • the network adapter card or network interface in each computing/processing device receives the computer-readable program instructions from the network and forwards the computer-readable program instructions for storage in the computer-readable storage medium in each computing/processing device.
  • the computer program instructions for performing the operation of the present invention may be assembly instructions, instruction set architecture (ISA) instructions, machine instructions, machine-related instructions, microcode, firmware instructions, state setting data, or source code or object code written in any combination of one or more programming languages, including object-oriented programming languages, such as Smalltalk, C++, Python, etc., and conventional procedural programming languages, such as "C" language or similar programming languages.
  • Computer-readable program instructions may be executed completely on a user's computer, partially on a user's computer, as an independent software package, partially on a user's computer, partially on a remote computer, or completely on a remote computer or server.
  • the remote computer may be connected to the user's computer via any type of network, including a local area network (LAN) or a wide area network (WAN), or may be connected to an external computer (e.g., using an Internet service provider to connect via the Internet).
  • an electronic circuit such as a programmable logic circuit, a field programmable gate array (FPGA), or a programmable logic array (PLA), may be personalized by utilizing the state information of the computer-readable program instructions, and the electronic circuit may execute the computer-readable program instructions, thereby realizing various aspects of the present invention.
  • These computer-readable program instructions can be provided to a processor of a general-purpose computer, a special-purpose computer, or other programmable data processing device, thereby producing a machine, so that when these instructions are executed by the processor of the computer or other programmable data processing device, a device that implements the functions/actions specified in one or more boxes in the flowchart and/or block diagram is generated.
  • These computer-readable program instructions can also be stored in a computer-readable storage medium, and these instructions cause the computer, programmable data processing device, and/or other equipment to work in a specific manner, so that the computer-readable medium storing the instructions includes a manufactured product, which includes instructions for implementing various aspects of the functions/actions specified in one or more boxes in the flowchart and/or block diagram.
  • Computer-readable program instructions may also be loaded onto a computer, other programmable data processing apparatus, or other device so that a series of operating steps are performed on the computer, other programmable data processing apparatus, or other device to produce a computer-implemented process, thereby causing the instructions executed on the computer, other programmable data processing apparatus, or other device to implement the functions/actions specified in one or more boxes in the flowchart and/or block diagram.
  • each box in the flowchart or block diagram can represent a module, a program segment or a part of an instruction, and the module, a program segment or a part of an instruction contains one or more executable instructions for realizing the specified logical function.
  • the functions marked in the box can also occur in a different order than the order marked in the accompanying drawings. For example, two consecutive boxes can actually be executed substantially in parallel, and they can sometimes be executed in the opposite order, depending on the functions involved.
  • each box in the block diagram and/or the flowchart, and the combination of the boxes in the block diagram and/or the flowchart can be implemented by a dedicated hardware-based system that performs the specified function or action, or can be implemented by a combination of dedicated hardware and computer instructions. It is well known to those skilled in the art that it is equivalent to implement it by hardware, implement it by software, and implement it by combining software and hardware.

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Abstract

A fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network, said method comprising: acquiring a cardiac magnetic resonance image; inputting the cardiac magnetic resonance image into a trained segmentation network, and segmenting a right ventricle region, a myocardial region, and a left ventricle region. The segmentation network is constructed on the basis of a residual network U-Net, and a bottleneck layer of the residual network adopts dilated convolution having a set dilation rate so as to combine an encoding path and a decoding path. According to the described method, the right ventricle, the left ventricle, the myocardium, and other regions can be accurately segmented from a cardiac magnetic resonance image, fully automatic segmentation of a heart image is achieved, and image segmentation performance of heart regions is improved.

Description

一种基于扩张残差网络的全自动心脏磁共振成像分割方法A fully automatic cardiac magnetic resonance imaging segmentation method based on dilated residual network 技术领域Technical Field
本发明涉及生物医学工程技术领域,更具体地,涉及一种基于扩张残差网络的全自动心脏磁共振成像分割方法。The present invention relates to the field of biomedical engineering technology, and more specifically, to a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network.
背景技术Background technique
心脏类疾病严重威胁人的生命,为了有效治疗和预防这类疾病,精准计算、建模和分析整个心脏结构对于医学领域的研究和应用至关重要。然而,在获得CMRI(磁共振电影成像)期间,心脏的不停跳动使得获得清晰图像的难度增大,尤其对于心血管疾病患者来说,更有可能经历心律失常,屏住呼吸困难等。这导致MRI(磁共振成像)扫描仪的图像可能包含各种图像伪影,从而难以评估图像质量。如果影像数据分割不正确,临床医生可能会从影像数据中得出错误的结论。现有的手工分割图像不仅耗时,而且精度难以保证。因此,需要实现心脏区域的自动分割用于解决心脏医疗领域的实际问题。Heart diseases seriously threaten human life. In order to effectively treat and prevent such diseases, accurate calculation, modeling and analysis of the entire heart structure are crucial for research and application in the medical field. However, during CMRI (cinema magnetic resonance imaging), the constant beating of the heart makes it more difficult to obtain clear images, especially for patients with cardiovascular diseases, who are more likely to experience arrhythmias, difficulty holding their breath, etc. This causes the images of MRI (magnetic resonance imaging) scanners to contain various image artifacts, making it difficult to evaluate image quality. If the image data is not segmented correctly, clinicians may draw incorrect conclusions from the image data. Existing manual segmentation of images is not only time-consuming, but also difficult to guarantee accuracy. Therefore, it is necessary to realize automatic segmentation of the heart area to solve practical problems in the field of cardiac medicine.
心脏图像分割是指将心脏图像划分为多个解剖学上有意义的区域,基于这些区域可以提取定量度量,例如心肌质量,壁厚,左心室(LV)和右心室(RV)的体积。因此,设计一种精准的全自动心脏分割算法尤为重要。近年来,深度卷积神经网络(DCNN)已被证明比传统的计算机视觉方法能更好地分割左、右心室和心肌。例如,U-Net体系结构是任务独立的,并已应用于各种生物医学分割任务,只需一些微小或实质性的修改,U-Net是大多数最有效的心室分割算法的基础网络模型(backbone)。Cardiac image segmentation refers to the division of cardiac images into multiple anatomically meaningful regions, based on which quantitative metrics such as myocardial mass, wall thickness, and the volumes of the left ventricle (LV) and right ventricle (RV) can be extracted. Therefore, it is particularly important to design an accurate and fully automatic cardiac segmentation algorithm. In recent years, deep convolutional neural networks (DCNNs) have been shown to be better than traditional computer vision methods at segmenting the left and right ventricles and myocardium. For example, the U-Net architecture is task-independent and has been applied to various biomedical segmentation tasks with only minor or substantial modifications. U-Net is the backbone of most of the most effective ventricle segmentation algorithms.
在现有技术中,专利申请CN202210321078.8提供了基于人工智能语义分割的CT图像心脏分割方法及系统。该技术通过对类别概率的优化减小了噪声的影响,实现了准确的图像分割。但该方案没有涉及到心脏中具体左心室、右心室、以及心肌间的分割问题,无法获得独立的心脏组织图 像。In the prior art, patent application CN202210321078.8 provides a CT image heart segmentation method and system based on artificial intelligence semantic segmentation. This technology reduces the impact of noise by optimizing the category probability and achieves accurate image segmentation. However, this solution does not involve the specific segmentation of the left ventricle, right ventricle, and myocardium in the heart, and cannot obtain independent heart tissue images.
专利申请CN202110391121.3描述了一种基于心脏MRI的心脏分割模型和病理分类模型训练、心脏分割、病理分类方法及装置,该技术能够极大抑制背景干扰,促进神经网络训练快速收敛,但针对图像分割精度和鲁棒性并未提出改进方法。Patent application CN202110391121.3 describes a cardiac segmentation model and pathology classification model training, cardiac segmentation, and pathology classification method and device based on cardiac MRI. This technology can greatly suppress background interference and promote rapid convergence of neural network training, but no improvement method is proposed for image segmentation accuracy and robustness.
经分析,现有技术缺乏对U-Net瓶颈层的研究,由于在图像中存在背景区域远大于掩膜的情况,因此伴随网络层数加深产生的像素退化、时间和空间信息的丢失问题导致了网络对于图像稀疏特征的提取能力不足。After analysis, it was found that the existing technology lacks research on the bottleneck layer of U-Net. Since the background area in the image is much larger than the mask, the pixel degradation and loss of time and space information caused by the deepening of the network layers lead to the network's insufficient ability to extract sparse features of the image.
发明内容Summary of the invention
本发明的目的是克服上述现有技术的缺陷,提供一种基于扩张残差网络的全自动心脏磁共振成像分割方法。该方法包括以下步骤:The purpose of the present invention is to overcome the defects of the prior art and provide a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network. The method comprises the following steps:
获取心脏磁共振图像;Obtain cardiac magnetic resonance images;
将所述心脏磁共振图像输入到经训练的分割网络,分割出右心室区域、心肌区域和左心室区域;Inputting the cardiac magnetic resonance image into a trained segmentation network to segment the right ventricle region, the myocardium region and the left ventricle region;
其中,所述分割网络基于残差网络U-Net构建,所述残差网络的瓶颈层采用设定扩张率的扩张卷积块来组合编码路径和解码路径。The segmentation network is constructed based on the residual network U-Net, and the bottleneck layer of the residual network adopts a dilated convolution block with a set dilation rate to combine the encoding path and the decoding path.
与现有技术相比,本发明的优点在于,提出一种基于扩张残差网络的全自动心脏MRI(磁共振成像)分割方法,能够从心脏MRI图像中精确分割右心室、左心室、心肌等区域,实现心脏图像的全自动分割,并且提高了心脏区域图像分割的性能。Compared with the prior art, the advantage of the present invention is that it proposes a fully automatic cardiac MRI (magnetic resonance imaging) segmentation method based on a dilated residual network, which can accurately segment the right ventricle, left ventricle, myocardium and other regions from cardiac MRI images, realize fully automatic segmentation of cardiac images, and improve the performance of cardiac region image segmentation.
通过以下参照附图对本发明的示例性实施例的详细描述,本发明的其它特征及其优点将会变得清楚。Further features and advantages of the present invention will become apparent from the following detailed description of exemplary embodiments of the present invention with reference to the attached drawings.
附图说明BRIEF DESCRIPTION OF THE DRAWINGS
被结合在说明书中并构成说明书的一部分的附图示出了本发明的实施例,并且连同其说明一起用于解释本发明的原理。The accompanying drawings, which are incorporated in and constitute a part of the specification, illustrate embodiments of the invention and, together with the description, serve to explain the principles of the invention.
图1是根据本发明一个实施例的基于扩张残差网络的全自动心脏磁共振成像分割方法的流程图;FIG1 is a flow chart of a fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network according to an embodiment of the present invention;
图2是根据本发明一个实施例的从原始磁共振图像数据到图像分割的过程示意图;FIG2 is a schematic diagram of a process from raw magnetic resonance image data to image segmentation according to an embodiment of the present invention;
图3是根据本发明一个实施例的基于U-Net的自动图像分割架构图;FIG3 is a diagram of an automatic image segmentation architecture based on U-Net according to an embodiment of the present invention;
图4是根据本发明一个实施例的扩张残差块的架构示意图;FIG4 is a schematic diagram of the architecture of an expanded residual block according to an embodiment of the present invention;
图5是根据本发明一个实施例的针对ACDC测试数据集的图像分割结果示意图;FIG5 is a schematic diagram of image segmentation results for an ACDC test data set according to an embodiment of the present invention;
附图中,Conv-卷积;Norm-正则化;Maxpool-最大池化;UpConv-上卷积;Deconvolution-解卷积;Skip-connection-跳跃连接;Pixel-wise addition-逐像素相加;Kernel-核;Concatenation-级联;Stride-步长;End Systole-心缩末期;End Diastole-心舒末期。In the attached figure, Conv-convolution; Norm-regularization; Maxpool-maximum pooling; UpConv-up convolution; Deconvolution-deconvolution; Skip-connection-skip connection; Pixel-wise addition-pixel-by-pixel addition; Kernel-kernel; Concatenation-cascade; Stride-stride; End Systole-end systole; End Diastole-end diastole.
具体实施方式Detailed ways
现在将参照附图来详细描述本发明的各种示例性实施例。应注意到:除非另外具体说明,否则在这些实施例中阐述的部件和步骤的相对布置、数字表达式和数值不限制本发明的范围。Various exemplary embodiments of the present invention will now be described in detail with reference to the accompanying drawings. It should be noted that the relative arrangement of components and steps, numerical expressions and numerical values set forth in these embodiments do not limit the scope of the present invention unless otherwise specifically stated.
以下对至少一个示例性实施例的描述实际上仅仅是说明性的,决不作为对本发明及其应用或使用的任何限制。The following description of at least one exemplary embodiment is merely illustrative in nature and is in no way intended to limit the invention, its application, or uses.
对于相关领域普通技术人员已知的技术、方法和设备可能不作详细讨论,但在适当情况下,所述技术、方法和设备应当被视为说明书的一部分。Technologies, methods, and equipment known to ordinary technicians in the relevant art may not be discussed in detail, but where appropriate, the technologies, methods, and equipment should be considered as part of the specification.
在这里示出和讨论的所有例子中,任何具体值应被解释为仅仅是示例性的,而不是作为限制。因此,示例性实施例的其它例子可以具有不同的值。In all examples shown and discussed herein, any specific values should be interpreted as merely exemplary and not limiting. Therefore, other examples of the exemplary embodiments may have different values.
应注意到:相似的标号和字母在下面的附图中表示类似项,因此,一旦某一项在一个附图中被定义,则在随后的附图中不需要对其进行进一步讨论。It should be noted that like reference numerals and letters refer to similar items in the following figures, and therefore, once an item is defined in one figure, it need not be further discussed in subsequent figures.
本发明通过结合短轴CMRI(磁共振电影成像)序列图像,开发了一种用于分割右心室(RV)、心肌(MYO)和左心室(LV)的全自动分割方法。该方法通过扩张卷积残差网络(DRN)来捕获U-Net中的多分辨率特征,从而显著增加了空间和时间信息并保持了定位精度。并且,将每个 扩展路径的输出逐像素相加以改善训练响应。The present invention develops a fully automatic segmentation method for right ventricle (RV), myocardium (MYO) and left ventricle (LV) by combining short-axis CMRI (cinema magnetic resonance imaging) sequence images. The method captures multi-resolution features in U-Net by dilating convolutional residual network (DRN), thereby significantly increasing spatial and temporal information and maintaining positioning accuracy. In addition, the output of each dilation path is added pixel by pixel to improve the training response.
结合图1和图2所示,所提供的基于扩张残差网络的全自动心脏磁共振成像分割方法包括以下步骤:As shown in FIG1 and FIG2 , the provided fully automatic cardiac magnetic resonance imaging segmentation method based on dilated residual network includes the following steps:
步骤S110,对数据集进行预处理,以获取训练样本。Step S110, preprocessing the data set to obtain training samples.
以利用磁共振电影成像为例,三维图像的尺寸为L×W×H,其中L为图像序列长度,W是图像的宽度,H是图像的长度。在数据集中,使用映射的方式将图像的标签值设置为四种标签,分别是:黑色背景=0,RV=1,MYO=2,LV=3。Taking magnetic resonance imaging as an example, the size of a three-dimensional image is L×W×H, where L is the length of the image sequence, W is the width of the image, and H is the length of the image. In the dataset, the image label values are set to four labels using a mapping method, namely: black background = 0, RV = 1, MYO = 2, LV = 3.
考虑到磁共振电影图像的显示空间尺寸H×W和强度分布的范围存在显著差异。在一个实施例中,通过数据预处理过程获取训练样本,具体地,以ACDC(Adverse Conditions Dataset with Correspondences)图像为例。首先,对输入的图像进行重采样。ACDC数据集存在体素间距问题,由于卷积神经网络无法解释体素间距,通过重新采样所有图像到相同的体素间距1.52×1.52×6.35mm。Considering that there are significant differences in the display space size H×W and the range of intensity distribution of magnetic resonance movie images. In one embodiment, training samples are obtained through a data preprocessing process. Specifically, ACDC (Adverse Conditions Dataset with Correspondences) images are taken as an example. First, the input image is resampled. The ACDC dataset has a voxel spacing problem. Since the convolutional neural network cannot explain the voxel spacing, all images are resampled to the same voxel spacing of 1.52×1.52×6.35mm.
数据预处理过程是考虑到体素间距直接影响图像的整体体素大小,也影响了卷积神经网络从图像补丁中提取的上下文信息量。此外,如果体素间距大幅增加,图像大小就会减小到细节丢失的程度,因此需要确保在网络补丁大小中包含的上下文信息数量和图像数据中保留的细节数量之间进行权衡,以获得最佳性能。The data preprocessing process takes into account that the voxel spacing directly affects the overall voxel size of the image, and also affects the amount of contextual information that the convolutional neural network can extract from the image patch. In addition, if the voxel spacing is greatly increased, the image size will be reduced to the point where details are lost, so it is necessary to ensure that there is a trade-off between the amount of contextual information included in the network patch size and the amount of detail retained in the image data to obtain the best performance.
在一个实施例中,对于训练数据,将所有图像重采样为256×256像素的中值。然后使用多层磁共振电影图像获得ACDC数据集的磁共振图像。例如,提取每个患者的2D-MRI(磁共振成像)切片及其相关注释。并对每个时间帧逐片执行归一化。In one embodiment, for training data, all images are resampled to a median of 256×256 pixels. Then, magnetic resonance images of the ACDC dataset are obtained using multi-layer magnetic resonance movie images. For example, 2D-MRI (magnetic resonance imaging) slices of each patient and their associated annotations are extracted. And normalization is performed slice by slice for each time frame.
步骤S120,通过数据增强扩充训练样本,并构建训练集。Step S120, expanding the training samples through data enhancement and constructing a training set.
由于训练数据有限,模型无法学习到期望的不变性和鲁棒性特征,从而导致过拟合。因此,可对训练数据应用多种数据增强技术来扩充样本数量。例如,采用基本图像变换技术,包括随机旋转、随机弹性变形、缩放、翻转和伽马校正。当应用于原始训练图像时,这种数据增强技术可以有效地生成相同图像的多个视图。通过采用多种数据增强方法扩充训练样本, 能够解决过拟合以及类不平衡问题。Due to limited training data, the model cannot learn the expected invariance and robustness features, resulting in overfitting. Therefore, a variety of data augmentation techniques can be applied to the training data to expand the number of samples. For example, basic image transformation techniques are used, including random rotation, random elastic deformation, scaling, flipping, and gamma correction. When applied to the original training images, this data augmentation technique can effectively generate multiple views of the same image. By using a variety of data augmentation methods to expand the training samples, overfitting and class imbalance problems can be solved.
步骤S130,构建基于扩张残差网络的分割网络。Step S130, constructing a segmentation network based on the dilated residual network.
在本文中,以采用U-net网络作为基础的心脏分割网络为例进行说明,参见图3和图4所示,其中图4对应图3的扩张残差块架构。从输入图像到最终输出,在整个分割过程,分割网络遵循编码器-解码器的整体架构。例如,使用5个编码块构造收缩路径;每个块由2个卷积层组成,具有3×3核和2×2最大池化操作,步长为2。最初,选择32个卷积核。在每一次最大池化操作之后,卷积核将增加,从而在U-Net的瓶颈层中产生320个卷积核。类似地,特征图的空间维度通过下采样操作减少了2倍。线性整流单元(ReLU)被带泄露线性整流替换,并且使用实例正则化而不是归一化(BN)。In this paper, a heart segmentation network based on the U-net network is used as an example for explanation, as shown in Figures 3 and 4, where Figure 4 corresponds to the dilated residual block architecture of Figure 3. From the input image to the final output, the segmentation network follows the overall architecture of the encoder-decoder throughout the segmentation process. For example, a contraction path is constructed using 5 encoding blocks; each block consists of 2 convolutional layers with 3×3 kernels and 2×2 maximum pooling operations with a stride of 2. Initially, 32 convolution kernels are selected. After each maximum pooling operation, the convolution kernel will increase, resulting in 320 convolution kernels in the bottleneck layer of the U-Net. Similarly, the spatial dimension of the feature map is reduced by a factor of 2 through a downsampling operation. The rectified linear unit (ReLU) is replaced by a leaky linear rectifier, and instance regularization is used instead of normalization (BN).
通过扩展残差网络(DRN)在U-Net瓶颈层组合编码和解码路径,该网络捕获全局上下文并恢复空间和时间信息,而不影响分割图的分辨率。此外,扩展残差网络可以有效地调整卷积层的深度,而不会降低网络性能。例如,通过使用具有不同扩张率(d=1、3和5)的扩张卷积,扩张残差网络块中的感受野被扩大。然后,通过残差连接将先前生成的特征与当前特征级联。在DRN(扩展残差网络)块中每3×3卷积之后,执行遗忘率为0.5的暂退(dropout)操作以防止过拟合。因此,扩展残差网络捕获上下文图像信息、高空间分辨率和多纹理特征。解码路径的过程类似于编码路径的过程,然而操作的顺序是相反的。U-Net架构提供了将编码的特征图从编码块重用到其对应级别的优点,其中空间维度匹配。这可以通过特定于信道的级联来实现。在解码路径的最后一级使用1×1内核投影操作,以将输出信道维度与所分类别(左心室、心肌和右心室)对齐。最后,通过上采样和逐像素相加聚合所有扩展路径输出,以增强训练响应。The encoding and decoding paths are combined at the U-Net bottleneck layer by a dilated residual network (DRN), which captures global context and recovers spatial and temporal information without affecting the resolution of the segmentation map. In addition, the dilated residual network can effectively adjust the depth of the convolutional layer without degrading the network performance. For example, the receptive field in the dilated residual network block is enlarged by using dilated convolutions with different dilation rates (d=1, 3, and 5). Then, the previously generated features are cascaded with the current features through residual connections. After each 3×3 convolution in the DRN (Diluted Residual Network) block, a dropout operation with a forgetting rate of 0.5 is performed to prevent overfitting. Therefore, the dilated residual network captures contextual image information, high spatial resolution, and multi-texture features. The process of the decoding path is similar to that of the encoding path, however, the order of operations is reversed. The U-Net architecture provides the advantage of reusing the encoded feature maps from the encoding block to its corresponding level, where the spatial dimensions match. This can be achieved through channel-specific cascading. A 1×1 kernel projection operation is used at the last level of the decoding path to align the output channel dimensions with the classified categories (left ventricle, myocardium, and right ventricle). Finally, all extended path outputs are aggregated by upsampling and pixel-wise addition to enhance the training response.
通常情况下,自然图像包含许多物体,它们的身份和相对位置对理解场景很重要。然而,当目标对象在空间上不突出时,例如,当目标对象与背景相比很小时,分割会变得更加困难。如果目标对象的特征在下采样过程中丢失,在训练中就不容易恢复。但如果在整个网络中保持高度(大量)的空间和时间信息,并提供密集覆盖输入特征的输出特征,反向传播可以 从较小和不太突出的对象中学习重要的特征。因此,本发明采用扩张卷积网络,通过增大感受野,提取更多的空间信息来预测小而密集的图像特征。离散的扩张卷积如下:Typically, natural images contain many objects whose identities and relative positions are important for understanding the scene. However, segmentation becomes more difficult when the target object is not spatially prominent, for example, when the target object is small compared to the background. If the features of the target object are lost during the downsampling process, they are not easy to recover during training. However, if a high (large) amount of spatial and temporal information is maintained throughout the network and output features that densely cover the input features are provided, backpropagation can learn important features from smaller and less prominent objects. Therefore, the present invention adopts an expanded convolutional network to extract more spatial information to predict small and dense image features by increasing the receptive field. The discrete expanded convolution is as follows:
Figure PCTCN2022131363-appb-000001
Figure PCTCN2022131363-appb-000001
其中,
Figure PCTCN2022131363-appb-000002
是输入和输出离散函数,k为大小为(2d+1) 2的离散核,* l为扩张卷积,在求和过程中,需满足s+lt=p,s表示扩张步幅,l表示缩放因子,p表示感受野,t表示整数序列,即t=1,2,3...n。
in,
Figure PCTCN2022131363-appb-000002
is a discrete function of input and output, k is a discrete kernel of size (2d+1) 2 , * l is a dilated convolution, and in the summation process, s+lt=p must be satisfied, s represents the dilation stride, l represents the scaling factor, p represents the receptive field, and t represents an integer sequence, that is, t=1,2,3...n.
一个扩张的残差网络可以更好地扩大感受野,以达到一个有希望的结果,并避免在U-Net的瓶颈处出现图像信息丢失。扩张卷积向卷积层引入了一个称为“扩张率(dilation rate)”的新参数,该参数定义了卷积核处理数据时各值的间距,通过添加空洞来扩大感受野。扩张卷积层是基于具有扩张因子(d=1、3和5)的常规卷积。例如,为普通卷积层选择1×1的核,为扩张卷积选择3×3的核。A dilated residual network can better expand the receptive field to achieve a promising result and avoid the loss of image information at the bottleneck of U-Net. Dilated convolution introduces a new parameter called "dilation rate" to the convolution layer, which defines the spacing between the values when the convolution kernel processes the data, expanding the receptive field by adding holes. The dilated convolution layer is based on the regular convolution with dilation factors (d = 1, 3 and 5). For example, a 1×1 kernel is selected for the regular convolution layer and a 3×3 kernel is selected for the dilated convolution.
Figure PCTCN2022131363-appb-000003
Figure PCTCN2022131363-appb-000003
其中,y ij表示输入为x ij的扩张卷积,它是具有长度为M,宽度为N的卷积核,m、n为扩张卷积的输入变量。w(i,j)为相应权值,i表示图像长度索引,j表示图像宽度索引,d表示扩张率。 Among them, y ij represents the dilated convolution with input x ij , which is a convolution kernel with length M and width N, and m and n are the input variables of the dilated convolution. w(i, j) is the corresponding weight, i represents the image length index, j represents the image width index, and d represents the dilation rate.
步骤S140,利用设定的损失函数训练分割网络。Step S140, training the segmentation network using the set loss function.
分割的目的是检测目标对象并在其周围绘制轮廓。自动分割轮廓Cp(预测的)与对应的标注图像进行比较,以测量所提出方法的精度。在本文中,由轮廓包围的像素称为A p和A gThe goal of segmentation is to detect the target object and draw a contour around it. The automatically segmented contour Cp (predicted) is compared with the corresponding annotated image to measure the accuracy of the proposed method. In this paper, the pixels surrounded by the contour are called A p and Ag .
在分割网络训练中,可采用多种损失函数。例如,骰子相似度系数或豪斯多夫距离或其他损失函数类型。There are many types of loss functions that can be used in segmentation network training, for example, Dice similarity coefficient or Hausdorff distance or other types of loss functions.
例如,对于骰子相似度系数(DSC),是预测轮廓和地面真实度轮廓之间的比率表示DSC得分,通常以0到1之间的百分比表示。高骰子值表示匹配良好。For example, for the Dice Similarity Coefficient (DSC), the ratio between the predicted silhouette and the ground truth silhouette represents the DSC score, usually expressed as a percentage between 0 and 1. A high Dice value indicates a good match.
Figure PCTCN2022131363-appb-000004
Figure PCTCN2022131363-appb-000004
其中,A p表示预测轮廓包围的像素,A g表示真实轮廓所包围的像素。 Among them, Ap represents the pixels surrounded by the predicted contour, and Ag represents the pixels surrounded by the real contour.
豪斯多夫距离(HD)是比较预测和实际轮廓之间的对称距离,并提供磁共振电影图像的空间分辨率。HD值越低,分割匹配性能越好。The Hausdorff distance (HD) is a symmetric distance between the predicted and actual contours and provides the spatial resolution of the MRI cine images. The lower the HD value, the better the segmentation matching performance.
Figure PCTCN2022131363-appb-000005
Figure PCTCN2022131363-appb-000005
其中,C p为预测的自动分割轮廓,C g为相应的真实标记轮廓,d(i,j)表示地面真实值与预测轮廓之间的距离,i表示预测轮廓的像素点,j表示地面真实轮廓的像素点。考虑到感兴趣区域(ROI)和背景之间的图像存在显著的类别不平衡。为了解决这个问题,测试了不同的损失函数,包括骰子损失和加权交叉熵损失。 Where Cp is the predicted automatically segmented contour, Cg is the corresponding true labeled contour, d(i, j) represents the distance between the ground truth and the predicted contour, i represents the pixel of the predicted contour, and j represents the pixel of the ground truth contour. Considering that there is a significant class imbalance in images between the region of interest (ROI) and the background. To address this issue, different loss functions are tested, including dice loss and weighted cross entropy loss.
在一个优选实施例中,使用包含骰子损失和交叉熵损失的双重损失函数来训练分割网络。具体地,交叉熵损失定义如下:In a preferred embodiment, a dual loss function including dice loss and cross entropy loss is used to train the segmentation network. Specifically, the cross entropy loss is defined as follows:
Figure PCTCN2022131363-appb-000006
Figure PCTCN2022131363-appb-000006
其中,C表示类别总数;c表示类别指示,W=(w 1,w 2,w 3...w n)是一系列的可学习权重,w n是第n层的权重矩阵;p(Y i|X i,W)表示一个预测的像素X i相对地面真值标签像素分类错误的概率;Y(c,x)表示对应于输入x的目标标签;
Figure PCTCN2022131363-appb-000007
表示对应于输入x的预测类别c的激活函数值。例如,对于c所表示的类别,黑色背景=0,RV=1,MYO=2,LV=3。
Where C represents the total number of categories; c represents the category indicator, W = (w 1 , w 2 , w 3 ... w n ) is a series of learnable weights, w n is the weight matrix of the nth layer; p(Y i |X i , W) represents the probability of a predicted pixel Xi being misclassified relative to the ground truth label pixel; Y(c, x) represents the target label corresponding to the input x;
Figure PCTCN2022131363-appb-000007
Represents the activation function value corresponding to the predicted category c of the input x. For example, for the category represented by c, black background = 0, RV = 1, MYO = 2, LV = 3.
该模型的训练共进行了500次迭代,在训练集的每次迭代中,从数据集中随机抽取250张图像直至遍历完所有的图像数据。为了提升泛化能力,从训练图像中随机裁剪了切片,并在验证集上的每次迭代之后对网络进行评估。例如,使用下式的骰子损失的多类变体来训练分割网络。The model was trained for a total of 500 iterations, where 250 images were randomly sampled from the dataset in each iteration of the training set until all the image data was exhausted. To improve generalization, slices were randomly cropped from the training images and the network was evaluated after each iteration on the validation set. For example, a multi-class variant of the dice loss was used to train the segmentation network.
Figure PCTCN2022131363-appb-000008
Figure PCTCN2022131363-appb-000008
其中,u和v是激活函数softmax输出的独热编码向量和类别识别符对应的图像分割标签值,i表示图像长度索引,k表示图像宽度索引;c∈C是类别识别符,即心脏的左心室、右心室、心肌和背景;ε是一个微小常数。在每次遍历之后,根据下式重新计算学习速率lr。最后,选择了最佳模型来评估测试集,以确保RV(右心室)、MYO(心肌)和LV(左心室)的验证达到了最高DSC(骰子相似度系数)。该网络在所有折叠中提供一致 且稳定的性能。Where u and v are the one-hot encoded vectors and the image segmentation label values corresponding to the class identifiers of the activation function softmax output, i represents the image length index, and k represents the image width index; c∈C is the class identifier, i.e., the left ventricle, right ventricle, myocardium, and background of the heart; ε is a tiny constant. After each traversal, the learning rate lr is recalculated according to the following formula. Finally, the best model is selected to evaluate the test set to ensure that the verification of RV (right ventricle), MYO (myocardium), and LV (left ventricle) achieves the highest DSC (Dice Similarity Coefficient). The network provides consistent and stable performance in all folds.
Figure PCTCN2022131363-appb-000009
Figure PCTCN2022131363-appb-000009
其中,initial_learning_rate为初始学习率,currentepoch为当前的迭代次数,totalepoch为全部的迭代次数。Among them, initial_learning_rate is the initial learning rate, currentepoch is the current number of iterations, and totalepoch is the total number of iterations.
步骤S150,针对采集的目标磁共振图像,利用经训练的分割网络识别出右心室、心肌和左心室等区域。Step S150, for the acquired target magnetic resonance image, using the trained segmentation network to identify regions such as the right ventricle, myocardium and left ventricle.
在完成分割网络的训练后,即可获得优化的模型参数,进而利用经训练的分割网络,可以准确区分右心室、心肌和左心室等感兴趣区域,以及完整的心脏轮廓,进而基于这些区域可以提取定量度量,例如心肌质量,左心室和右心室的体积等。After completing the training of the segmentation network, the optimized model parameters can be obtained. Then, using the trained segmentation network, the regions of interest such as the right ventricle, myocardium and left ventricle, as well as the complete heart contour can be accurately distinguished. Then, based on these regions, quantitative measurements can be extracted, such as myocardial mass, the volume of the left and right ventricles, etc.
为进一步验证本发明的效果,已在多个患者心脏磁共振图像上进行了实验测试。参见图5所示的心脏不同切片位置的示意图。实验结果表明,本发明获得了较高的左心室、右心室及心肌的分割精度和分割速度,获得了0.92±0.02的总体骰子相似度系数和8.06±0.05mm的平均豪斯多夫距离。并且,本发明提高了图像分割的速度,例如,处理2D磁共振图像平均需要0.28秒。此外,本发明的网络设计用于预测单独的磁共振图像,以分割心室区域,成功实现了心脏图像的自动分割。To further verify the effect of the present invention, experimental tests have been carried out on cardiac magnetic resonance images of multiple patients. See the schematic diagram of different heart slice positions shown in Figure 5. The experimental results show that the present invention achieves higher segmentation accuracy and segmentation speed of the left ventricle, right ventricle and myocardium, and obtains an overall dice similarity coefficient of 0.92±0.02 and an average Hausdorff distance of 8.06±0.05mm. In addition, the present invention improves the speed of image segmentation, for example, it takes an average of 0.28 seconds to process 2D magnetic resonance images. In addition, the network design of the present invention is used to predict a separate magnetic resonance image to segment the ventricular region, and successfully achieves automatic segmentation of cardiac images.
综上所述,相对于现有技术,本发明具有以下技术效果:In summary, compared with the prior art, the present invention has the following technical effects:
1)本发明引入了扩张卷积残差网络,对U-Net瓶颈层进行了性能增强,以实现心脏MRI(磁共振成像)图像的全自动精准分割,解决了U-Net瓶颈层的限制,显著增强了空间和时间信息,在保持空间一致性的同时提高精度。1) The present invention introduces a dilated convolutional residual network and enhances the performance of the U-Net bottleneck layer to achieve fully automatic and accurate segmentation of cardiac MRI (magnetic resonance imaging) images, which solves the limitations of the U-Net bottleneck layer, significantly enhances spatial and temporal information, and improves accuracy while maintaining spatial consistency.
2)本发明设计了扩展残差网络(DRN)块,以替换U-Net原始的瓶颈层。并且使用了多种损失函数,以在分割心脏图像过程中更好的利用心脏特征训练模型,提高精度。2) The present invention designs an extended residual network (DRN) block to replace the original bottleneck layer of U-Net, and uses a variety of loss functions to better utilize cardiac features to train the model and improve accuracy in the process of segmenting cardiac images.
3)本发明具有更高的计算速度和鲁棒性,可以应用于多样化的心脏CMRI(磁共振电影成像)数据集。例如,处理的数据为患者在两种不同磁强度下的磁共振图像,数据经处理后可同时得到患者的完整心脏轮廓,左右心室以及心肌轮廓的图像。3) The present invention has higher computing speed and robustness, and can be applied to a variety of cardiac CMRI (cine magnetic resonance imaging) data sets. For example, the processed data is a patient's magnetic resonance image at two different magnetic intensities, and after the data is processed, the patient's complete heart contour, left and right ventricles, and myocardial contour images can be obtained simultaneously.
本发明可以是系统、方法和/或计算机程序产品。计算机程序产品可以包括计算机可读存储介质,其上载有用于使处理器实现本发明的各个方面的计算机可读程序指令。The present invention may be a system, a method and/or a computer program product. The computer program product may include a computer-readable storage medium carrying computer-readable program instructions for causing a processor to implement various aspects of the present invention.
计算机可读存储介质可以是可以保持和存储由指令执行设备使用的指令的有形设备。计算机可读存储介质例如可以是但不限于电存储设备、磁存储设备、光存储设备、电磁存储设备、半导体存储设备或者上述的任意合适的组合。计算机可读存储介质的更具体的例子(非穷举的列表)包括:便携式计算机盘、硬盘、随机存取存储器(RAM)、只读存储器(ROM)、可擦式可编程只读存储器(EPROM或闪存)、静态随机存取存储器(SRAM)、便携式压缩盘只读存储器(CD-ROM)、数字多功能盘(DVD)、记忆棒、软盘、机械编码设备、例如其上存储有指令的打孔卡或凹槽内凸起结构、以及上述的任意合适的组合。这里所使用的计算机可读存储介质不被解释为瞬时信号本身,诸如无线电波或者其他自由传播的电磁波、通过波导或其他传输媒介传播的电磁波(例如,通过光纤电缆的光脉冲)、或者通过电线传输的电信号。Computer readable storage medium can be a tangible device that can hold and store instructions used by an instruction execution device. Computer readable storage medium can be, for example, but not limited to, an electrical storage device, a magnetic storage device, an optical storage device, an electromagnetic storage device, a semiconductor storage device, or any suitable combination thereof. More specific examples (non-exhaustive list) of computer readable storage medium include: a portable computer disk, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), a static random access memory (SRAM), a portable compact disk read-only memory (CD-ROM), a digital versatile disk (DVD), a memory stick, a floppy disk, a mechanical encoding device, for example, a punch card or a convex structure in a groove on which instructions are stored, and any suitable combination thereof. The computer readable storage medium used here is not interpreted as a transient signal itself, such as a radio wave or other freely propagating electromagnetic wave, an electromagnetic wave propagated by a waveguide or other transmission medium (for example, a light pulse by an optical fiber cable), or an electrical signal transmitted by a wire.
这里所描述的计算机可读程序指令可以从计算机可读存储介质下载到各个计算/处理设备,或者通过网络、例如因特网、局域网、广域网和/或无线网下载到外部计算机或外部存储设备。网络可以包括铜传输电缆、光纤传输、无线传输、路由器、防火墙、交换机、网关计算机和/或边缘服务器。每个计算/处理设备中的网络适配卡或者网络接口从网络接收计算机可读程序指令,并转发该计算机可读程序指令,以供存储在各个计算/处理设备中的计算机可读存储介质中。The computer-readable program instructions described herein can be downloaded from a computer-readable storage medium to each computing/processing device, or downloaded to an external computer or external storage device via a network, such as the Internet, a local area network, a wide area network, and/or a wireless network. The network can include copper transmission cables, optical fiber transmissions, wireless transmissions, routers, firewalls, switches, gateway computers, and/or edge servers. The network adapter card or network interface in each computing/processing device receives the computer-readable program instructions from the network and forwards the computer-readable program instructions for storage in the computer-readable storage medium in each computing/processing device.
用于执行本发明操作的计算机程序指令可以是汇编指令、指令集架构(ISA)指令、机器指令、机器相关指令、微代码、固件指令、状态设置数据、或者以一种或多种编程语言的任意组合编写的源代码或目标代码,所述编程语言包括面向对象的编程语言—诸如Smalltalk、C++、Python等,以及常规的过程式编程语言—诸如“C”语言或类似的编程语言。计算机可读程序指令可以完全地在用户计算机上执行、部分地在用户计算机上执行、作为一个独立的软件包执行、部分在用户计算机上部分在远程计算机上执 行、或者完全在远程计算机或服务器上执行。在涉及远程计算机的情形中,远程计算机可以通过任意种类的网络—包括局域网(LAN)或广域网(WAN)—连接到用户计算机,或者,可以连接到外部计算机(例如利用因特网服务提供商来通过因特网连接)。在一些实施例中,通过利用计算机可读程序指令的状态信息来个性化定制电子电路,例如可编程逻辑电路、现场可编程门阵列(FPGA)或可编程逻辑阵列(PLA),该电子电路可以执行计算机可读程序指令,从而实现本发明的各个方面。The computer program instructions for performing the operation of the present invention may be assembly instructions, instruction set architecture (ISA) instructions, machine instructions, machine-related instructions, microcode, firmware instructions, state setting data, or source code or object code written in any combination of one or more programming languages, including object-oriented programming languages, such as Smalltalk, C++, Python, etc., and conventional procedural programming languages, such as "C" language or similar programming languages. Computer-readable program instructions may be executed completely on a user's computer, partially on a user's computer, as an independent software package, partially on a user's computer, partially on a remote computer, or completely on a remote computer or server. In the case of a remote computer, the remote computer may be connected to the user's computer via any type of network, including a local area network (LAN) or a wide area network (WAN), or may be connected to an external computer (e.g., using an Internet service provider to connect via the Internet). In some embodiments, an electronic circuit, such as a programmable logic circuit, a field programmable gate array (FPGA), or a programmable logic array (PLA), may be personalized by utilizing the state information of the computer-readable program instructions, and the electronic circuit may execute the computer-readable program instructions, thereby realizing various aspects of the present invention.
这里参照根据本发明实施例的方法、装置(系统)和计算机程序产品的流程图和/或框图描述了本发明的各个方面。应当理解,流程图和/或框图的每个方框以及流程图和/或框图中各方框的组合,都可以由计算机可读程序指令实现。Various aspects of the present invention are described herein with reference to the flow charts and/or block diagrams of the methods, devices (systems) and computer program products according to embodiments of the present invention. It should be understood that each box of the flow chart and/or block diagram and the combination of each box in the flow chart and/or block diagram can be implemented by computer-readable program instructions.
这些计算机可读程序指令可以提供给通用计算机、专用计算机或其它可编程数据处理装置的处理器,从而生产出一种机器,使得这些指令在通过计算机或其它可编程数据处理装置的处理器执行时,产生了实现流程图和/或框图中的一个或多个方框中规定的功能/动作的装置。也可以把这些计算机可读程序指令存储在计算机可读存储介质中,这些指令使得计算机、可编程数据处理装置和/或其他设备以特定方式工作,从而,存储有指令的计算机可读介质则包括一个制造品,其包括实现流程图和/或框图中的一个或多个方框中规定的功能/动作的各个方面的指令。These computer-readable program instructions can be provided to a processor of a general-purpose computer, a special-purpose computer, or other programmable data processing device, thereby producing a machine, so that when these instructions are executed by the processor of the computer or other programmable data processing device, a device that implements the functions/actions specified in one or more boxes in the flowchart and/or block diagram is generated. These computer-readable program instructions can also be stored in a computer-readable storage medium, and these instructions cause the computer, programmable data processing device, and/or other equipment to work in a specific manner, so that the computer-readable medium storing the instructions includes a manufactured product, which includes instructions for implementing various aspects of the functions/actions specified in one or more boxes in the flowchart and/or block diagram.
也可以把计算机可读程序指令加载到计算机、其它可编程数据处理装置、或其它设备上,使得在计算机、其它可编程数据处理装置或其它设备上执行一系列操作步骤,以产生计算机实现的过程,从而使得在计算机、其它可编程数据处理装置、或其它设备上执行的指令实现流程图和/或框图中的一个或多个方框中规定的功能/动作。Computer-readable program instructions may also be loaded onto a computer, other programmable data processing apparatus, or other device so that a series of operating steps are performed on the computer, other programmable data processing apparatus, or other device to produce a computer-implemented process, thereby causing the instructions executed on the computer, other programmable data processing apparatus, or other device to implement the functions/actions specified in one or more boxes in the flowchart and/or block diagram.
附图中的流程图和框图显示了根据本发明的多个实施例的系统、方法和计算机程序产品的可能实现的体系架构、功能和操作。在这点上,流程图或框图中的每个方框可以代表一个模块、程序段或指令的一部分,所述模块、程序段或指令的一部分包含一个或多个用于实现规定的逻辑功能的可执行指令。在有些作为替换的实现中,方框中所标注的功能也可以以不 同于附图中所标注的顺序发生。例如,两个连续的方框实际上可以基本并行地执行,它们有时也可以按相反的顺序执行,这依所涉及的功能而定。也要注意的是,框图和/或流程图中的每个方框、以及框图和/或流程图中的方框的组合,可以用执行规定的功能或动作的专用的基于硬件的系统来实现,或者可以用专用硬件与计算机指令的组合来实现。对于本领域技术人员来说公知的是,通过硬件方式实现、通过软件方式实现以及通过软件和硬件结合的方式实现都是等价的。The flowcharts and block diagrams in the accompanying drawings show the possible architecture, functions and operations of the systems, methods and computer program products according to multiple embodiments of the present invention. In this regard, each box in the flowchart or block diagram can represent a module, a program segment or a part of an instruction, and the module, a program segment or a part of an instruction contains one or more executable instructions for realizing the specified logical function. In some alternative implementations, the functions marked in the box can also occur in a different order than the order marked in the accompanying drawings. For example, two consecutive boxes can actually be executed substantially in parallel, and they can sometimes be executed in the opposite order, depending on the functions involved. It should also be noted that each box in the block diagram and/or the flowchart, and the combination of the boxes in the block diagram and/or the flowchart can be implemented by a dedicated hardware-based system that performs the specified function or action, or can be implemented by a combination of dedicated hardware and computer instructions. It is well known to those skilled in the art that it is equivalent to implement it by hardware, implement it by software, and implement it by combining software and hardware.
以上已经描述了本发明的各实施例,上述说明是示例性的,并非穷尽性的,并且也不限于所披露的各实施例。在不偏离所说明的各实施例的范围和精神的情况下,对于本技术领域的普通技术人员来说许多修改和变更都是显而易见的。本文中所用术语的选择,旨在最好地解释各实施例的原理、实际应用或对市场中的技术改进,或者使本技术领域的其它普通技术人员能理解本文披露的各实施例。本发明的范围由所附权利要求来限定。Embodiments of the present invention have been described above, and the above description is exemplary, not exhaustive, and is not limited to the disclosed embodiments. Many modifications and variations will be apparent to those of ordinary skill in the art without departing from the scope and spirit of the described embodiments. The selection of terms used herein is intended to best explain the principles of the embodiments, practical applications, or technical improvements in the marketplace, or to enable other persons of ordinary skill in the art to understand the embodiments disclosed herein. The scope of the present invention is defined by the appended claims.

Claims (10)

  1. 一种基于扩张残差网络的全自动心脏磁共振成像分割方法,包括以下步骤:A fully automatic cardiac magnetic resonance imaging segmentation method based on a dilated residual network comprises the following steps:
    获取心脏磁共振图像;Obtain cardiac magnetic resonance images;
    将所述心脏磁共振图像输入到经训练的分割网络,分割出右心室区域、心肌区域和左心室区域;Inputting the cardiac magnetic resonance image into a trained segmentation network to segment the right ventricle region, the myocardium region and the left ventricle region;
    其中,所述分割网络基于残差网络U-Net构建,所述残差网络的瓶颈层采用设定扩张率的扩张卷积块来组合编码路径和解码路径。The segmentation network is constructed based on the residual network U-Net, and the bottleneck layer of the residual network adopts a dilated convolution block with a set dilation rate to combine the encoding path and the decoding path.
  2. 根据权利要求1所述的方法,其特征在于,所述分割网络根据以下步骤训练:The method according to claim 1, characterized in that the segmentation network is trained according to the following steps:
    构建训练集,所述训练集包含多条样本数据,每条样本数据是附有标注类别的磁共振图像,该标注类别用于区分右心室区域、心肌区域和左心室区域;Constructing a training set, wherein the training set includes a plurality of sample data, each of which is a magnetic resonance image with a labeled category, and the labeled category is used to distinguish the right ventricular region, the myocardial region, and the left ventricular region;
    对所述训练集进行图像增强,以针对相同磁共振图像生成多个视图,所述图像增强包括随机旋转、随机弹性变形、缩放、翻转和伽马校正中的一项或多项;Performing image enhancement on the training set to generate multiple views for the same magnetic resonance image, wherein the image enhancement includes one or more of random rotation, random elastic deformation, scaling, flipping, and gamma correction;
    利用图像增强后的训练集,以设定的损失函数训练所述分割网络,获得优化的参数。The segmentation network is trained using the image-enhanced training set with a set loss function to obtain optimized parameters.
  3. 根据权利要求1所述的方法,其特征在于,以设定的损失函数训练所述分割网络包括:The method according to claim 1, characterized in that training the segmentation network with a set loss function comprises:
    在设定到迭代次数范围内,利用交叉熵损失函数训练分割网络,每次迭代从所述训练集中抽取设定数量的样本图像;Within a set number of iterations, the segmentation network is trained using a cross entropy loss function, and a set number of sample images are extracted from the training set in each iteration;
    从训练图像中随机裁剪切片,并在验证集上的每次迭代之后对分割网络进行评估,并使用骰子损失的多类变体来训练分割网络;Randomly crop clips from the training images and evaluate the segmentation network after each iteration on the validation set. The segmentation network is trained using a multi-class variant of the Dice loss.
    在每次遍历之后,重新计算学习速率;After each epoch, the learning rate is recalculated;
    选择满足设定性能要求的分割网络作为所述经训练的分割网络。A segmentation network that meets the set performance requirements is selected as the trained segmentation network.
  4. 根据权利要求3所述的方法,其特征在于,所述交叉熵损失表示为:The method according to claim 3, characterized in that the cross entropy loss is expressed as:
    Figure PCTCN2022131363-appb-100001
    Figure PCTCN2022131363-appb-100001
    其中,C表示标注类别总数;c表示标注类别指示,W=(w 1,w 2,w 3...w n)是一系列的待学习权重,w n是第n层的权重矩阵,p(Y i|X i,W)表示一个预测的像素X i相对地面真值标签像素Y i分类错误的概率,Y(c,x)表示对应于输入x的目标标签;
    Figure PCTCN2022131363-appb-100002
    表示对应于输入x的预测类别c的激活函数值。
    Where C represents the total number of labeled categories; c represents the labeled category indicator, W = (w 1 , w 2 , w 3 ... w n ) is a series of weights to be learned, w n is the weight matrix of the nth layer, p(Y i |X i , W) represents the probability of a predicted pixel Xi being misclassified relative to the ground truth label pixel Yi , and Y(c, x) represents the target label corresponding to the input x;
    Figure PCTCN2022131363-appb-100002
    represents the activation function value corresponding to the predicted category c of input x.
  5. 根据权利要求3所述的方法,其特征在于,所述骰子损失表示为:The method according to claim 3, characterized in that the dice loss is expressed as:
    Figure PCTCN2022131363-appb-100003
    Figure PCTCN2022131363-appb-100003
    其中,u和v是激活函数softmax输出的独热编码向量和标注类别指示c∈C对应的图像分割标签值,i表示图像长度索引,k表示图像宽度索引,ε是设定常数,C表示标注类别总数。Among them, u and v are the one-hot encoding vectors output by the activation function softmax and the image segmentation label values corresponding to the annotation category indication c∈C, i represents the image length index, k represents the image width index, ε is a set constant, and C represents the total number of annotation categories.
  6. 根据权利要求3所述的方法,其特征在于,根据以下公式更新所述学习率:The method according to claim 3, characterized in that the learning rate is updated according to the following formula:
    Figure PCTCN2022131363-appb-100004
    Figure PCTCN2022131363-appb-100004
    其中,initial_learning_rate为初始学习率,currentepoch为当前的迭代次数,totalepoch为全部的迭代次数。Among them, initial_learning_rate is the initial learning rate, currentepoch is the current number of iterations, and totalepoch is the total number of iterations.
  7. 根据权利要求1所述的方法,其特征在于,所述分割网络的解码路径的最后一级使用1×1内核投影操作。The method of claim 1, wherein the last stage of the decoding path of the segmentation network uses a 1×1 kernel projection operation.
  8. 根据权利要求1所述的方法,其特征在于,所述扩张率设置为d=1、3或5。The method according to claim 1, characterized in that the expansion rate is set to d=1, 3 or 5.
  9. 一种计算机可读存储介质,其上存储有计算机程序,其中,该计算机程序被处理器执行时实现根据权利要求1至8中任一项所述的方法的步骤。A computer-readable storage medium having a computer program stored thereon, wherein the computer program, when executed by a processor, implements the steps of the method according to any one of claims 1 to 8.
  10. 一种计算机设备,包括存储器和处理器,在所述存储器上存储有能够在处理器上运行的计算机程序,其特征在于,所述处理器执行所述计算机程序时实现权利要求1至8中任一项所述的方法的步骤。A computer device comprises a memory and a processor, wherein a computer program that can be run on the processor is stored in the memory, and wherein the processor implements the steps of any one of the methods of claims 1 to 8 when executing the computer program.
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