Differentiation of Recurrence from Radiation Necrosis in Gliomas Based on the Radiomics of Combinational Features and Multimodality MRI Images

Zhang, Quan; Cao, Jianyun; Zhang, Junde; Bu, Junguo; Yu, Yuwei; Tan, Yujing; Feng, Qianjin; Huang, Meiyan

doi:https://doi.org/10.1155/2019/2893043

Computational and Mathematical Methods in Medicine

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Abstract Introduction Materials and Methods Discussion Abbreviations Data Availability Conflicts of Interest Authors’ Contributions Acknowledgments Supplementary Materials References Copyright Related Articles

Research Article | Open Access

Volume 2019 | Article ID 2893043 | https://doi.org/10.1155/2019/2893043

Differentiation of Recurrence from Radiation Necrosis in Gliomas Based on the Radiomics of Combinational Features and Multimodality MRI Images

Quan Zhang,¹Jianyun Cao,^1,2Junde Zhang,²Junguo Bu,²Yuwei Yu,¹Yujing Tan,²Qianjin Feng,¹and Meiyan Huang¹

Academic Editor: Valeri Makarov

Received18 Jul 2019

Revised16 Oct 2019

Accepted31 Oct 2019

Published01 Dec 2019

Abstract

Purpose. To classify radiation necrosis versus recurrence in glioma patients using a radiomics model based on combinational features and multimodality MRI images. Methods. Fifty-one glioma patients who underwent radiation treatments after surgery were enrolled in this study. Sixteen patients revealed radiation necrosis while 35 patients showed tumor recurrence during the follow-up period. After treatment, all patients underwent T1-weighted, T1-weighted postcontrast, T2-weighted, and fluid-attenuated inversion recovery scans. A total of 41,284 handcrafted and 24,576 deep features were extracted for each patient. The 0.623 + bootstrap method and the area under the curve (denoted as 0.632 + bootstrap AUC) metric were used to select the features. The stepwise forward method was applied to construct 10 logistic regression models based on different combinations of image features. Results. For handcrafted features on multimodality MRI, model 7 with seven features yielded the highest AUC of 0.9624, sensitivity of 0.8497, and specificity of 0.9083 in the validation set. These values were higher than the accuracy of using handcrafted features on single-modality MRI (paired t-test, , except sensitivity). For combined handcrafted and AlexNet features on multimodality MRI, model 6 with six features achieved the highest AUC of 0.9982, sensitivity of 0.9941, and specificity of 0.9755 in the validation set. These values were higher than the accuracy of using handcrafted features on multimodality MRI (paired t-test, ). Conclusions. Handcrafted and deep features extracted from multimodality MRI images reflecting the heterogeneity of gliomas can provide useful information for glioma necrosis/recurrence classification.

1. Introduction

Gliomas are the most common and aggressive brain tumors in adults and have an approximate 5-year survival rate of 10% in their highest grade (e.g., glioblastoma multiforme) [1]. The conventional therapy for gliomas is surgery followed by conventional radiotherapy/chemotherapy [1, 2]. However, this combinatory therapy usually leads to radiation necrosis, which is the most common side effect in gliomas within 2 years after treatment [3, 4]. Unfortunately, the period of occurrence of radiation necrosis is also the peak period of glioma recurrence [4]. Clinically, the methods used to distinguish between glioma recurrence and necrosis are follow-up, biopsy, and surgical resection [5]. Given that the treatment protocols of glioma necrosis and recurrence are quite different [6, 7], finding a fast and noninvasive way to differentiate glioma necrosis from recurrence is important.

Radiomics [8] is widely used as a noninvasive method to classify lesions into recurrence or necrosis [9, 10]. In the current radiomics models, good classification results are achieved by using handcrafted features (e.g., intensity and texture features). However, handcrafted features are shallow and low-ordered; as such, they may not fully characterize tumor heterogeneity and, in fact, could limit the potential of the radiomics model applied [11]. To solve this problem, a number of studies have proposed the use of deep features [12–15]. In these studies, improvements in performance were observed by incorporating deep features into the radiomics model of interest. Thus, exploiting potential tumor heterogeneity by using deep features is expected to provide a new and effective point of view from which to improve glioma necrosis and recurrence classification.

Frequent monitoring is required for cancer patients; among the imaging methods available, MRI is consistently the preferred technique [16]. Different MRI modalities, such as magnetic resonance spectroscopy [17, 18], T1-weighted postcontrast (T1C) imaging [19], and diffusion-weighted imaging [20], are used to differentiate glioma necrosis from recurrence. However, most previous studies employ image information from single-modality MRI. Moreover, during follow-up, the most commonly used scans for glioma patients are T1-weighted (T1), T1C, T2-weighted (T2), and fluid-attenuated inversion recovery (FLAIR) images. Single-modality MRI provides partial information, whereas multimodality MRI comprehensively characterizes tissues [21, 22]. Therefore, combining different MRI modalities can enhance the tumor discriminatory power of the technology and reveal the degree of tumor infiltration [21, 23, 24]. Figure 1 shows that the heterogeneities of glioma recurrence and necrosis in different MRI modalities are different.

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In this study, we proposed a novel radiomics model for distinguishing necrosis versus glioma recurrence. The contributions of our study were as follows. First, multimodality MRI images were used in this research. Different MRI modalities could reveal different parts of the tumor area [22]. Therefore, the accuracy of glioma identification could be improved by using multimodality MRI images [25]. Second, deep features were combined with handcrafted features in this study to classify glioma necrosis versus recurrence. The powerful ability of deep features has been verified in previous studies [13–15]. Moreover, to the best of our knowledge, previous studies have not combined multimodality MRI images and deep features for classifying glioma necrosis versus recurrence. Therefore, the proposed method might be a valuable tool for distinguishing glioma necrosis from recurrence.

2. Materials and Methods

2.1. Study Population and MRI Images

This retrospective study was supported by the ethics committee of hospital and written informed consent was waived.

In this study, the diagnosis of glioma recurrence and necrosis was confirmed by two neuroradiologists with work experiences of over 9 and 20 years. Patients were included on the basis of the following criteria: (1) pathologically confirmed that glioma recurrence or necrosis occurred after radiotherapy; (2) all glioma patients’ recurrence or necrosis after radiotherapy was confirmed by imaging and clinical follow-up (follow-up time > 6 months); (3) all MRI images (T1, T1C, T2, and FLAIR images) of glioma necrosis and recurrence used must be confirmed at a follow-up of no less than 6 months after radiotherapy; and (4) glioma patients without pathologic diagnosis excluded the possibility of pseudoprogression based on follow-up. If the follow-up time was not enough, it was difficult for the neuroradiologist to judge whether the patient has recurrence or pseudoprogression. Such glioma patients were not accepted. The exclusion criteria were as follows: (1) patients with recurrent glioma without radiotherapy; (2) follow-up time of less than 6 months for glioma patients; and (3) glioma patients without four modalities of MRI images. A total of 51 patients (16 necrosis and 35 recurrences) were enrolled in this study. The clinical characteristics of all patients are summarized in Table 1.

MRI images were obtained by using 3.0 T MRI machines (Philips, Achieva). The MRI protocols for the four modalities are listed in Table 2. All MRI scans were obtained in the axial plane. Figure 1 illustrates an example of the four modalities of MRI images of glioma recurrence and necrosis.

2.2. Overview of the Proposed Method

The overall framework of the proposed method is shown in Figure 2. The method consists of three fundamental steps: (1) an image preprocessing step that obtains tumor regions, (2) a feature extraction step that extracts handcrafted and deep features, and (3) an analysis step that combines univariate and multivariate analyses. This combination allows the selection of features and construction of a prediction model for glioma necrosis and recurrence classification.

2.2.1. Image Preprocessing

We used the linear registration function in FSL5.0.9 (http://fsl.fmrib.ox.ac.uk) to register T1, T2, and FLAIR images to T1C images and then applied ITK-SNAP software (http://www.itk-snap.org) to manually segment the tumor region for each patient. All manual segmentations of the tumor region were drawn slice-by-slice by a neuroradiologist with over 9 years of experience in neuroradiology. To avoid mistakes, another senior neuroradiologist with 20 years of experience in brain tumor diagnosis confirmed the final tumor region. All segmentations were drawn on T1C images, covered the entire tumor (avoid cystic changes, edema, and blood vessels), and used to extract handcrafted and deep features.

2.2.2. Feature Extraction

The methodology used to extract handcrafted features from the tumor region and texture extraction parameters is described in the Supplementary Information. A total of 4 nontexture and 41,280 texture parameter features (10,320 features from each image of each MRI modality) were extracted for each patient.

We selected AlexNet [26] and Inception v3 [27], which were pretrained on approximately 1.2 million images from the ImageNet Dataset. Features were obtained by forward propagating an MRI slice through the network and extracting the deep features. The architectures of both networks are illustrated in the Supplementary Information. In our glioma dataset, the number of glioma lesion slices and the size of the glioma lesion area in each slice were different for different patients. If we used all slices of a glioma lesion for each patient, the feature dimension would be varied across different patients. Therefore, a 3D bounding box was used to extract the tumor region and then to extract the axial slice with the largest tumor area from this box. We also extracted the front and back slices of the extracted slice. Finally, the three axial slices were combined as an RGB volume. AlexNet and Inception v3 network were a continuous convolution and pooling operation on the input images. Compared with the shallower layer of the two networks, more heterogeneous information of tumors can be extracted in the deeper layer. Moreover, the penultimate layer of the deep network had been used to extract deep features in some recent studies [15, 28, 29], and good performance could be achieved, which indicated the effectiveness of the deep features extracted from the deeper layers. Therefore, for AlexNet, the RGB volume was converted into a size of 227 × 227 × 3 as the input, and the penultimate layer (FC7) was used as the output. A total of 16,384 AlexNet features (4,096 features from each image of each MRI modality) were found. For Inception v3, the RGB volume was adjusted to a size of 299 × 299 × 3 as the final input, and the average pooling layer was used as the output. Therefore, a total of 8,192 Inception v3 features (2048 features from each image of each MRI modality) were drawn.

2.2.3. Univariate and Multivariable Analyses

Univariate associations between feature sets (4 nontexture features, 41,280 texture features, 16,384 AlexNet features, and 8,192 Inception v3 features) and glioma necrosis or recurrence were assessed using Spearman’s rank correlation . Given the existence of multiple comparisons, Bonferroni correction was also applied. The significance level was set to , where is the number of comparisons and is the significance level set to 0.05.

In multivariate analysis, our goal is to find a linear combination of interesting features so that whether the output is necrosis or recurrence for the new input data could be properly judged. Therefore, the prediction model was constructed by using a logistic regression model:where is the j th input variable (image features) of i th patient and is the regression coefficient of the model for a total of N patients.

We employed the 0.623 + bootstrap method and the area under the curve (denoted as 0.632 + bootstrap AUC) metric to estimate which model learned from our dataset could best classify glioma recurrence and necrosis on a new sample. Before presenting the estimation method, we provide a brief symbol introduction. Let our image dataset be denoted as . We construct a bootstrap sample with N patients randomly drawn with replacement from x. An original sample that does not appear in the bootstrap sample was defined as . The generation of a large number B (B = 1000) of randomly drawn bootstrap samples (b = 1, 2, …, B) is used to estimate a statistical quantity of interest on the unknown true population distribution. Note that the probability of selecting a positive (necrosis group class) is made equal to the probability of selecting a negative (recurrence group class) each time by drawing from x; this approach is called “imbalance-adjusted bootstrap resampling.”

Prediction models were constructed for three different types of initial feature sets: (1) four sets of single-modality handcrafted features (T1, T1C, T2, and FLAIR), including 10,320 texture and 4 nontexture features for each modality; (2) multimodality handcrafted features, including 41,280 texture and 4 nontexture features; and (3) two sets of multimodality deep features, including 16,384 AlexNet features and 8,192 Inception v3 features. However, the number of feature sets being too large, many redundant and irrelevant features would cause overfitting. Therefore, feature reduction was applied to reduce feature dimensionality. We then used the 0.632 + bootstrap method AUC metric to select features to construct different orders of regression models. Finally, we selected the optimal model from the constructed models for classification. We provide details of each step in the following sections.

(1) Feature Reduction. The feature set reduction was performed by a stepwise forward feature selection scheme in order to create reduced feature sets containing 25 different features from larger initial sets, a procedure carried out using the gain equation: where and .

In equation (2), is Spearman’s rank correlation coefficient between each feature j and the output vector , is the maximal information coefficient between features c and j [30], d is the selected feature for the reduced feature set, and D is the feature that has not been removed from the initial feature set. Parameters , , and are set to 0.5, 0.5, and 0, respectively. During each iteration, a new feature with the largest gain value is selected for the reduced feature set, after which a new gain can be calculated based on the features reserved from the initial feature set using imbalance-adjusted bootstrap resampling (B = 1,000). The final selected 25 features are arranged in descending order according to their gain value because the gain equation uses r_s varying over the whole feature set.

(2) Feature Selection. After feature reduction, we obtained 25 features for each of the three initial feature sets. We then combined the deep features obtained from AlexNet and Inception v3 features with the handcrafted features from multimodality MRI images to obtain 50 fusion features (denoted as fusion AlexNet and fusion Inception v3 features). Using the reduced feature sets, stepwise forward feature selection was performed by maximizing the 0.632 + bootstrap AUC. The order of the regression model was set from 1 to 10, where the order value is the number of features to be selected. For a given model order, 25 independent experiments were conducted for each of the three initial feature sets and 50 independent experiments were performed for each of the two fusion feature sets. In each independent experiment, different features from the reduced set were assigned as a different “starter.” For each given starter, 1,000 logistic regression models were first created for the remaining features by using imbalance-adjusted bootstrap resampling. Then, the single feature maximizing the 0.632 + bootstrap AUC, defined in equation (3), was selected. This process was repeated up to order 10, after which the combination of features yielding the highest 0.632 + bootstrap AUC for each model was identified. To clarify, we used 1-order regression model as an example. For the 25 selected features, each of them could be utilized to construct a 1-order regression model, and thus, there were 25 1-order regression models. For a given 1-order regression model, we first resampled the sample 1000 times to get 1000 pairs of training sets and validation sets. Then, 1000 experiments were carried out and the average of AUC of 1000 experiments was obtained for the model. Therefore, for a 1-order regression model, we got 25 averaged AUC values. For the 2–10 order features, the same process was performed as above. Finally, we selected the order corresponding to the maximum averaged AUC value as the final feature combination for the classification of glioma necrosis versus recurrence.where

(3) Classification Model Construction. After feature selection, the optimal combination of features was obtained for models of different orders. Imbalance-adjusted bootstrap resampling was performed for all models once more, and the 0.632 + bootstrap AUC of these models was calculated to select the optimal model.

To construct the final prediction model, the coefficients of the optimal combination of features were calculated as follows:where is the coefficient of feature j and can be calculated by solving the logistic regression model in equation (1), p is the model order, and j = 0 refers to the offset of model .

Using the calculated , the output of the optimal model could be obtained by using equation (1), and the final prediction score could be defined as

We employed equation (6) to convert the response of the model into a probabilistic form of output.

2.3. Implementation

In this study, all experiments were implemented on a standard personal computer with a single-thread Intel (R) Xeon (R) E5-2667 v4 3.2 GHz processor. The MATLAB 2017b packages used to analyze the radiomics data were available at https://cn.mathworks.com/matlabcentral/fileexchange/51948-radiomics. AlexNet and Inception v3 were pretrained and included in MATLAB 2017b.

Since our dataset was relatively small, the 0.632 + bootstrap resampling method has been used. The principle of this method was to resample all data. For a sample, the selected probability was assumed to be n, and the not being selected probability was 1−n. For the whole data, if we resampled n times, the not being selected probability of a sample was . When n was large enough, could be obtained, and thus, the selected probability of a sample was 1−0.368 = 0.632. In our experiments, we resampled the original dataset 1000 times and obtained 1000 training sets, so some samples of the original dataset might have appeared multiple times in a training set, and those did not appear eventually formed a validation set. Therefore, after resampling, 1000 pairs of training sets and validation sets could be generated. The number of samples in a training set was , and the number of samples in a validation set was . Classification performance was first evaluated in the training set and then confirmed in the validation set.

3. Univariate and Multivariable Results

The r_s values between the features and glioma recurrence versus necrosis, along with the corresponding values, are listed in Table 3. In the table, only nontexture features and a portion of the texture and deep features are listed. Other detailed r_s results of handcrafted features are provided in the Supplementary Information. In Table 3, for handcrafted features, such as gray-level run-length matrix (GLRLM)-HGRE and gray-level size zone matrix (GLSZM)-(HGZE, SZLGE, and SZHGE), extracted from the T1C, T2, and FLAIR images, have a slightly higher correlation with glioma recurrence versus necrosis. For deep features, a certain Spearman’s rank correlation with glioma necrosis versus recurrence is observed.

Figure 3 shows the prediction performance of the proposed method for the estimation of multivariable models with optimal feature combinations, which were obtained for each model order of the three original feature sets (including T1, T1C, T2, FLAIR, multimodality, AlexNet, and Inception v3 feature sets) and the two fusion feature sets (including fusion AlexNet and fusion Inception v3 feature sets). In Figure 3, the multimodality handcrafted features yielded the highest AUC of 0.9624, sensitivity of 0.8497, and specificity of 0.9083 in model 7 of validation set compared to the single-modality handcrafted features (paired t-test, , except sensitivity). Model 6 with six features (four handcrafted and two AlexNet features) yielded the highest AUC of 0.9982 in the validation set. Details of the classification accuracy of the optimal model on the training and validation sets are shown in Table 4. The selected features and response map of the optimal model for each feature set are given in the Supplemental Information.

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Figure 3

Estimation of the classification performance of multivariable models constructed from T1C, T2, T1, FLAIR, multimodality, AlexNet, Inception v3, fusion AlexNet, and fusion Inception v3 images using optimal features in the training set (a) and validation set (b) for the model orders 1–10. The optimal degrees of freedom were separately found in terms of the maximum 0.632 + bootstrap AUC for each model order. Error bars represent the standard error of the mean at the 95% confidence interval.

4. Discussion

In this study, we proposed a novel radiomics model that is expected to support the classification of glioma recurrence versus necrosis. In the proposed method, MRI images of four modalities (i.e., T1, T2, T1C, and FLAIR images) are used to extract handcrafted and deep features. Fifty-one cases of glioma necrosis and recurrence were applied to validate the proposed method. More importantly, we have obtained the highest classification accuracy on the validation set by using fusion AlexNet features from the perspective of classification accuracy and interpretability of features. Therefore, the proposed method might be a valuable tool for distinguishing glioma necrosis from recurrence.

We employed radiomics to distinguish glioma necrosis from recurrence. We first evaluated the performance of handcrafted features extracted from multimodality and single-modality MRI images. Table 4 shows that the classification accuracy of multimodality MRI is higher than that of single-modality MRI (paired t-test , except for AUC and sensitivity in T1 modality), which reveals the usefulness of employing different MRI modalities for the current task. However, the extraction methods for handcrafted features are similar for different types of lesions [31–36] and, thus, may limit the potential of radiomics [11]. In order to better reflect the heterogeneity of tumors and improve the performance of radiomics, some scholars have proposed the use of deep features. Antropova et al. [13] used the VGG19 model trained on natural images to extract the deep features of breast cancer and combined it with handcrafted features for the classification of breast cancer, and the results were greatly improved compared with handcrafted features; Decuyper et al. [12] used the trained VGG11 network to extract deep features for different inputs (ROI or the whole image) and classify the grade of glioma into two categories. In addition, Oikonomou et al. [8] show that the combination of handcrafted and deep features leads to the highest performance in lung cancer survival prediction using Random Forest and Naive Bayes classifiers. This successful application of deep features [12–14] confirms the validity of using deep features in our study.

We employed two CNNs (AlexNet and Inception v3) to extract deep features from multimodality MRI images to evaluate the effectiveness of these images for the classification work. In this study, we only extracted features from a given layer of a CNN rather than fine-tuning or training from scratch. Doing so can save computational time [13] and avoid the difficulty in designing CNN. Table 4 reveals that the classification accuracy of using AlexNet and Inception v3 features is higher than that of employing handcrafted features (paired t-test ). This finding further illustrates the usefulness of deep features in the classification of glioma necrosis versus recurrence. Table 4 also demonstrates that the classification accuracy of using AlexNet features is higher than that of using Inception v3 features (paired t-test ). The high performance of AlexNet may be due to its simple structure. Complex networks are designed for a specific task; thus, the generalized performance of a complex network is poorer than that of a simple network [13, 37]. Regardless of the performance of deep features, they are less interpretable than handcrafted features, which include tumor shape, volume, texture, and other descriptive features. Therefore, combining deep and handcrafted features provides more information on the object of interest. Finally, we built a six-order model based on the combination of AlexNet and multimodality handcrafted features, ultimately obtaining an AUC of 0.9982, a sensitivity of 0.9941, and a specificity of 0.9755.

Table 5 shows that the classification results of the proposed method outperform the results of recently published papers. Here, only the results of different methods in the literature are listed. Direct comparison of the performances of different methods is unreasonable because various datasets and methods for extracting features and building classifiers are used among studies. Nonetheless, the proposed method shows the highest AUC, specificity, and accuracy among the methods surveyed for the classification problem, thereby implying its advantage for classifying glioma recurrence and necrosis.

The proposed method presents certain limitations. First, the correlations among features were ignored. Despite finding that these correlations could contribute to the model, high-dimensional features were, in general, difficult to handle. Second, there were tens of thousands of features. However, these high-dimensional features were reduced by a stepwise forward feature selection scheme that reduces each of the initial feature sets to only 25 different features through the gain equation (2). Third, the dataset used in this study was relatively small, which was also the problem identified in previous studies [1, 38–42]. Therefore, a large patient cohort was necessary to create a more robust model. In this study, the bootstrap resampling method was used due to the small size of the dataset. We first resampled the whole sample 1000 times and then got 1000 training and validation sets, respectively. For each run of the 1000 experiments, we measured the AUC, sensitivity, and specificity for the training and the validation sets, respectively. Results show that all measurements of the training and the validation sets for each experiment were above 0.8 after combining the deep and the handcrafted features. In order to intuitively show the classification results of glioma necrosis versus recurrence, we used six-order AlexNet deep features and handcrafted features to conduct 1000 experiments as an example. Figure 4 shows the AUC values of the classification of glioma necrosis versus recurrence. The x-axis represented the number of the experiments, and the y-axis was the AUC values of the training and validation sets, respectively, measured by each experiment. It can be seen from Figure 4 that the variation tendency of the AUC of the validation sets was the same as that of the training sets, and the difference between the AUC values of the training and validation sets was very small, which indicated that overfitting on the proposed method was alleviated in this study.

In conclusion, finding a noninvasive and accurate method to classify glioma recurrence versus necrosis is clinically significant. In this study, we explored a novel method by combining deep and handcrafted features extracted from multimodality MRI images to improve the classification accuracy of glioma recurrence versus necrosis. Classification models based on objective and quantitative handcrafted and deep features can be useful for precision medicine and improve the treatment strategies used for glioma necrosis and recurrence.

Abbreviations

T1C:	T1-weighted postcontrast
T1:	T1-weighted
T2:	T2-weighted
FLAIR:	Fluid-attenuated inversion recovery
GLRLM:	Gray-level run-length matrix
GLSZM:	Gray-level size zone matrix
GLCM:	Gray-level co-occurrence matrix
NGTDM:	Neighbourhood gray-tone difference matrix 0.623 + bootstrap method and the area under the curve metric: 0.632 + bootstrap AUC

Data Availability

The data used to support the findings of this study are available from the corresponding author upon request.

Conflicts of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Authors’ Contributions

Quan Zhang and Jianyun Cao authors contributed equally to this work.

Acknowledgments

This work was supported by the National Natural Science Foundation of China (grant no. 81601562), the Science and Technology Planning Project of Guangzhou (grant no. 201904010417), and the Science and Technology Planning Project of Guangdong Province, China (grant no. 2015B010131011).

Supplementary Materials

Supplementary Material 1: methodology used to extract handcrafted features and texture extraction parameters. Supplementary Material 2: outline of the AlexNet and Inception v3 network architectures. Supplementary Material 3: Figures and Tables of experimental results. (Supplementary Materials)

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Copyright © 2019 Quan Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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