CN116205844A - A Fully Automatic Cardiac MRI Segmentation Method Based on Expanded Residual Networks - Google Patents
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Abstract
本发明公开了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。该包括:获取心脏磁共振图像;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,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。本发明能够从心脏磁共振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。
The invention discloses a fully automatic heart magnetic resonance imaging segmentation method based on an expanded residual network. This includes: acquiring a cardiac magnetic resonance image; inputting the cardiac magnetic resonance image into a trained segmentation network to segment the right ventricle area, myocardial area and left ventricle area, wherein the segmentation network is constructed based on the residual network U-Net , the bottleneck layer of the residual network uses an expansion convolution block with a set expansion rate to combine the encoding path and the decoding path. The invention can accurately segment regions such as right ventricle, left ventricle and myocardium from cardiac magnetic resonance images, realize automatic segmentation of cardiac images, and improve the performance of cardiac region image segmentation.
Description
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 invention relates to the technical field of biomedical engineering, and more specifically, to a fully automatic cardiac magnetic resonance imaging segmentation method based on an expanded 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 are a serious threat to human life. In order to effectively treat and prevent such diseases, accurate calculation, modeling and analysis of the entire heart structure are essential for research and application in the medical field. However, during CMRI (Magnetic Resonance Cine Imaging) acquisition, the beating heart makes it difficult to obtain clear images, especially for patients with cardiovascular disease, who are more likely to experience arrhythmia, difficulty in holding their breath, etc. As a result, images from MRI (magnetic resonance imaging) scanners may contain various image artifacts, making it difficult to assess image quality. Clinicians may draw wrong conclusions from imaging data if the imaging data is not properly segmented. The existing manual image segmentation is not only time-consuming, but also difficult to guarantee the accuracy. Therefore, it is necessary to realize the automatic segmentation of cardiac regions 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 anatomically meaningful regions based on which quantitative measures such as myocardial mass, wall thickness, left ventricle (LV) and right ventricle (RV) volumes can be extracted. Therefore, it is particularly important to design an accurate automatic heart segmentation algorithm. In recent years, deep convolutional neural networks (DCNNs) have been shown to segment left and right ventricles and myocardium better than traditional computer vision methods. For example, the U-Net architecture is task-independent and has been applied to various biomedical segmentation tasks with only some minor or substantial modifications, and U-Net is the underlying network model for most of the most effective ventricular segmentation algorithms ( backbone).
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 influence of noise by optimizing the class probability, and realizes accurate image segmentation. However, this solution does not involve the 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 pathological classification model training, cardiac segmentation, and pathological classification method and device based on cardiac MRI. This technology can greatly suppress background interference and promote rapid convergence of neural network training. However, for image Segmentation accuracy and robustness did not suggest improvements.
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, 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 the loss of time and space information caused by the deepening of the network layer lead to The network has insufficient ability to extract sparse features of images.
发明内容Contents 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 above-mentioned prior art, and to provide a fully automatic cardiac magnetic resonance imaging segmentation method based on an expanded residual network. The method includes 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;The cardiac magnetic resonance image is input to the trained segmentation network to segment the right ventricle area, myocardial area and left ventricle area;
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。Wherein, the segmentation network is constructed based on the residual network U-Net, and the bottleneck layer of the residual network uses an expansion convolution block with a set expansion 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 present invention has the advantage of proposing a fully automatic cardiac MRI (magnetic resonance imaging) segmentation method based on the expanded residual network, which can accurately segment the right ventricle, left ventricle, myocardium, etc. from cardiac MRI images region, to achieve fully automatic segmentation of heart images, and to improve the performance of heart 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。Other features of the present invention and advantages thereof will become apparent from the following detailed description of exemplary embodiments of the present invention with reference to the accompanying drawings.
附图说明Description of 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 this 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;Fig. 1 is a flow chart of a fully automatic cardiac magnetic resonance imaging segmentation method based on an expanded 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;Fig. 2 is a schematic diagram of the 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;Fig. 3 is a U-Net-based automatic image segmentation architecture diagram according to one 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;Fig. 4 is a schematic diagram of an 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;Fig. 5 is a schematic diagram of the image segmentation results for the ACDC test data set according to one 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 figure, Conv-convolution; Norm-regularization; Maxpool-maximum pooling; UpConv-convolution; Deconvolution-deconvolution; Skip-connection-jump connection; Pixel-wise addition-pixel-by-pixel addition; Kernel - Nucleus; Concatenation - cascade; Stride - step length; 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 arrangements of components and steps, numerical expressions and numerical values set forth in these embodiments do not limit the scope of the present invention unless specifically stated otherwise.
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 in no way taken as limiting 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。Techniques, methods and devices known to those of ordinary skill in the relevant art may not be discussed in detail, but where appropriate, such techniques, methods and devices should be considered part of the description.
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 construed as exemplary only, and not as limitations. Therefore, other instances of the exemplary embodiment 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 numerals and letters denote like items in the following figures, therefore, once an item is defined in one figure, it does not require further discussion 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 segmenting right ventricle (RV), myocardium (MYO) and left ventricle (LV) by combining short-axis CMRI (cine magnetic resonance imaging) sequence images. This method captures multi-resolution features in U-Net by dilating convolutional residual network (DRN), which significantly increases spatial and temporal information and maintains localization accuracy. And, the output of each expansion path is summed 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 Figure 1 and Figure 2, the provided fully automatic cardiac magnetic resonance imaging segmentation method based on the expanded 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 cine imaging as an example, the size of the 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 data set, the label value of the image is set to four labels by means of mapping, 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 ConditionsDataset 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 MRI cine 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. There is a voxel spacing problem in the ACDC dataset. 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 is to take into account that the voxel spacing directly affects the overall voxel size of the image, and also affects the amount of contextual information extracted by the convolutional neural network from the image patch. Furthermore, if the voxel spacing is increased substantially, the image size decreases to such an extent that details are lost, so it is necessary to ensure that there is a trade-off between the amount of contextual information contained in the network patch size and the amount of detail preserved in the image data to obtain the best results. 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 the training data, all images are resampled to a median of 256x256 pixels. Magnetic resonance images of the ACDC dataset were then acquired using the multislice magnetic resonance cine images. For example, extract 2D-MRI (magnetic resonance imaging) slices and their associated annotations for each patient. And perform normalization on a slice-by-slice basis for each timeframe.
步骤S120,通过数据增强扩充训练样本,并构建训练集。Step S120, expanding training samples through data augmentation, 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 the limited training data, the model cannot learn the desired invariant and robust features, resulting in overfitting. Therefore, various data augmentation techniques can be applied to the training data to expand the sample size. For example, basic image transformation techniques are employed, including random rotation, random elastic deformation, scaling, flipping, and gamma correction. When applied to original training images, this data augmentation technique can efficiently generate multiple views of the same image. By using a variety of data enhancement methods to expand the training samples, the problems of overfitting and class imbalance 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 expanded 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 article, the heart segmentation network based on the U-net network is used as an example to illustrate, as shown in Figure 3 and Figure 4, where Figure 4 corresponds to the expanded 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, the shrinkage path is constructed using 5 encoding blocks; each block consists of 2 convolutional layers with 3×3 kernels and 2×2 max-pooling operations with a stride of 2. Initially, 32 convolution kernels are selected. After each max pooling operation, the convolution kernels will be increased, resulting in 320 convolution kernels in the bottleneck layer of U-Net. Similarly, the spatial dimension of feature maps is reduced by a factor of 2 through the downsampling operation. The rectified linear unit (ReLU) is replaced by a leaky linear rectification, 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 bottleneck layer of U-Net by extending the residual network (DRN), which captures the global context and recovers the spatial and temporal information without compromising the resolution of the segmentation map. In addition, the extended residual network can effectively adjust the depth of the convolutional layer without degrading the network performance. For example, by using dilated convolutions with different dilation rates (d = 1, 3, and 5), the receptive field in the dilated residual network block is enlarged. Then, the previously generated features are concatenated with the current features via residual connections. After every 3×3 convolution in the DRN (Dilated Residual Network) block, a dropout operation with a forgetting rate of 0.5 is performed to prevent overfitting. Therefore, the extended 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 offers the advantage of reusing encoded feature maps from encoding blocks to their corresponding levels, where the spatial dimensions match. This can be achieved through channel-specific cascading. A 1×1 kernel projection operation is used at the last stage of the decoding path to align the output channel dimensions to the classified classes (left ventricle, myocardium, and right ventricle). Finally, all expansion path outputs are aggregated via 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 salient, for example, when the target object is small compared to the background. If the features of the target object are lost during downsampling, they cannot be easily recovered during training. But if highly (substantial) spatial and temporal information is maintained throughout the network and provided output features that densely cover input features, backpropagation can learn important features from smaller and less prominent objects. Therefore, the present invention uses an expanded convolutional network to predict small and dense image features by increasing the receptive field and extracting more spatial information. The discrete dilated convolution is as follows:
其中,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, Is the input and output discrete function, k is the discrete kernel of size (2d+1) 2 , * l is the expansion convolution, in the summation process, it needs to satisfy s+lt=p, s represents the expansion step, l represents Scaling factor, p represents the receptive field, t represents the sequence of integers, 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 image information loss at the bottleneck of U-Net. Dilated convolution introduces a new parameter called "dilation rate" to the convolutional layer, which defines the distance between values when the convolution kernel processes data, and expands the receptive field by adding holes. Dilated convolutional layers are based on regular convolutions with dilation factors (d=1, 3 and 5). For example, choose a 1×1 kernel for a normal convolutional layer and a 3×3 kernel for a dilated convolution.
其中,yij表示输入为xij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 expanded convolution whose input is x ij , which is a convolution kernel with a length of M and a width of N, and m and n are the input variables of the expanded 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, using the set loss function to train the segmentation network.
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Ap和Ag。The purpose of segmentation is to detect target objects and draw contours around them. 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 outline are referred to as A p and A g .
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。In segmentation network training, a variety of loss functions can be employed. For example, dice similarity coefficient or Hausdorff distance or other loss function types.
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 profile and the ground truth profile represents the DSC score, usually expressed as a percentage between 0 and 1. A high dice value indicates a good match.
其中,Ap表示预测轮廓包围的像素,Ag表示真实轮廓所包围的像素。Among them, A p represents the pixels surrounded by the predicted contour, and A g 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。Hausdorff distance (HD) is the symmetric distance between predicted and actual contours compared and provides spatial resolution of MR cine images. The lower the HD value, the better the segmentation matching performance.
其中,Cp为预测的自动分割轮廓,Cg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。Among them, C p is the predicted automatic segmentation contour, C g is the corresponding ground truth contour, d(i, j) represents the distance between the ground truth value and the predicted contour, i represents the pixel point of the predicted contour, and j represents the ground truth Contour pixels. Consider images with significant class imbalance between regions of interest (ROI) and background. To address this issue, different loss functions were 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, the segmentation network is trained using a dual loss function comprising dice loss and cross-entropy loss. Specifically, the cross-entropy loss is defined as follows:
其中,C表示类别总数;c表示类别指示,W=(w1,w2,w3...wn)是一系列的可学习权重,wn是第n层的权重矩阵;p(Yi|Xi,W)表示一个预测的像素Xi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;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。Among them, C represents the total number of categories; c represents the category indication, 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 that a predicted pixel X i is misclassified relative to the ground truth label pixel; Y(c, x) represents the target label corresponding to the input x; Indicates the activation function value corresponding to the predicted category c of the input x. For example, for the class 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 training of the model was carried out for 500 iterations in total. In each iteration of the training set, 250 images were randomly selected from the data set until all the image data were traversed. To improve generalization, slices are randomly cropped from the training images and the network is evaluated after each iteration on the validation set. For example, train a segmentation network using a multiclass variant of the dice loss of
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。Among them, u and v are the one-hot encoded vector output by the activation function softmax and the image segmentation label value corresponding to the category identifier, i represents the image length index, k represents the image width index; c∈C is the category identifier, that is, the left side of the heart Ventricle, right ventricle, myocardium and background; ε is a small constant. After each pass, the learning rate lr is recalculated according to the following formula. Finally, the best model was selected to evaluate the test set to ensure that the validation of RV (right ventricle), MYO (myocardium) and LV (left ventricle) achieved the highest DSC (Dice Similarity Coefficient). The network provides consistent and stable performance across all folds.
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 , using the trained segmentation network to identify regions such as right ventricle, myocardium, and left ventricle for the acquired target magnetic resonance image.
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, and then the trained segmentation network can be used to accurately distinguish the regions of interest such as the right ventricle, myocardium and left ventricle, as well as the complete heart contour, and then based on these regions can be Extract quantitative measures such as myocardial mass, left and right ventricle volumes, 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。In order to further verify the effect of the present invention, experimental tests have been carried out on cardiac magnetic resonance images of multiple patients. See Figure 5 for a schematic diagram of different slice positions of the heart. Experimental results show that the present invention obtains higher segmentation accuracy and segmentation speed of 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. Moreover, the present invention improves the speed of image segmentation, for example, it takes 0.28 seconds on average to process a 2D magnetic resonance image. Furthermore, our network designed to predict individual MRI images to segment ventricular regions successfully achieved 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 an expanded convolutional residual network, and enhances the performance of the U-Net bottleneck layer to realize fully automatic and accurate segmentation of cardiac MRI (magnetic resonance imaging) images, which solves the limitation of the U-Net bottleneck layer, Spatial and temporal information is significantly enhanced, improving 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 the Extended Residual Network (DRN) block to replace the original bottleneck layer of U-Net. And a variety of loss functions are used to better use the cardiac features to train the model and improve the accuracy in the process of segmenting the cardiac image.
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 calculation speed and robustness, and can be applied to diverse cardiac CMRI (magnetic resonance film imaging) data sets. For example, the processed data is the magnetic resonance images of the patient under two different magnetic intensities. After the data is processed, the patient's complete heart outline, images of the left and right ventricles and myocardial outline can be obtained at the same time.
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 can be a system, method and/or computer program product. A computer program product may include a computer readable storage medium having computer readable program instructions thereon 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。A computer readable storage medium may be a tangible device that can retain and store instructions for use by an instruction execution device. A computer readable storage medium may be, for example, but is 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 of the foregoing. More specific examples (a non-exhaustive list) of computer-readable storage media include: portable computer diskettes, hard disks, random access memory (RAM), read-only memory (ROM), erasable programmable read-only memory (EPROM), or flash memory), static random access memory (SRAM), compact disc read only memory (CD-ROM), digital versatile disc (DVD), memory stick, floppy disk, mechanically encoded device, such as a printer with instructions stored thereon A hole card or a raised structure in a groove, and any suitable combination of the above. As used herein, computer-readable storage media are not to be construed as transient signals per se, such as radio waves or other freely propagating electromagnetic waves, electromagnetic waves propagating through waveguides or other transmission media (e.g., pulses of light through fiber optic cables), or transmitted electrical signals.
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。Computer-readable program instructions described herein may be downloaded from a computer-readable storage medium to a respective computing/processing device, or downloaded to an external computer or external storage device over a network, such as the Internet, a local area network, a wide area network, and/or a wireless network. The network may include copper transmission cables, fiber optic transmission, wireless transmission, routers, firewalls, switches, gateway computers, and/or edge servers. A network adapter card or a network interface in each computing/processing device receives computer-readable program instructions from the network and forwards the computer-readable program instructions for storage in a 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。Computer program instructions for carrying out operations 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 or object code written in any combination, including object-oriented programming languages—such as Smalltalk, C++, Python, etc., and conventional procedural programming languages—such as the “C” language or similar programming languages. Computer readable program instructions may execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, partly on the user's computer and partly on a remote computer, or entirely on the remote computer or server implement. In cases involving a remote computer, the remote computer can be connected to the user computer through any kind of network, including a local area network (LAN) or a wide area network (WAN), or it can be connected to an external computer (such as via the Internet using an Internet service provider). connect). In some embodiments, an electronic circuit, such as a programmable logic circuit, field programmable gate array (FPGA), or programmable logic array (PLA), can be customized by utilizing state information of computer-readable program instructions, which can Various aspects of the invention are implemented by executing computer readable program instructions.
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。Aspects of the present invention are described herein with reference to flowchart illustrations and/or block diagrams of methods, apparatus (systems) and computer program products according to embodiments of the invention. It should be understood that each block of the flowcharts and/or block diagrams, and combinations of blocks in the flowcharts and/or block diagrams, 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 may be provided to a processor of a general purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine such that when executed by the processor of the computer or other programmable data processing apparatus , producing an apparatus for realizing the functions/actions specified in one or more blocks in the flowchart and/or block diagram. These computer-readable program instructions can also be stored in a computer-readable storage medium, and these instructions cause computers, programmable data processing devices and/or other devices to work in a specific way, so that the computer-readable medium storing instructions includes An article of manufacture comprising instructions for implementing various aspects of the functions/acts specified in one or more blocks in flowcharts and/or block diagrams.
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。It is also possible to load computer-readable program instructions into a computer, other programmable data processing device, or other equipment, so that a series of operational steps are performed on the computer, other programmable data processing device, or other equipment to produce a computer-implemented process , so that instructions executed on computers, other programmable data processing devices, or other devices implement the functions/actions specified in one or more blocks in the flowcharts and/or block diagrams.
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 flowchart and block diagrams in the figures illustrate the architecture, functionality, and operation of possible implementations of systems, methods and computer program products according to various embodiments of the present invention. In this regard, each block in a flowchart or block diagram may represent a module, a portion of a program segment, or an instruction that includes one or more Executable instructions. In some alternative implementations, the functions noted in the block may occur out of the order noted in the figures. For example, two blocks in succession may, in fact, be executed substantially concurrently, or they may sometimes be executed in the reverse order, depending upon the functionality involved. It should also be noted that each block of the block diagrams and/or flowchart illustrations, and combinations of blocks in the block diagrams and/or flowchart illustrations, can be implemented by a dedicated hardware-based system that performs the specified function or action , or may be implemented by a combination of dedicated hardware and computer instructions. It is well known to those skilled in the art that implementation by means of hardware, implementation by means of software, and implementation by a combination of software and hardware are all equivalent.
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。Having described various embodiments of the present invention, the foregoing description is exemplary, not exhaustive, and is not limited to the disclosed embodiments. Many modifications and alterations will be apparent to those of ordinary skill in the art without departing from the scope and spirit of the described embodiments. The terminology used herein is chosen to best explain the principle of each embodiment, practical application or technical improvement in the market, or to enable other ordinary skilled in the art to understand each embodiment disclosed herein. The scope of the invention is defined by the appended claims.
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