Efficient and accurate segmentation of the rectum in images acquired with a low-field (58-74mT), prostate Magnetic Resonance Imaging (MRI) scanner may be advantageous for MRI-guided prostate biopsy and focal treatment guidance. However, automated rectum segmentation on low-field MRI images is challenging due to spatial resolution and signal-to-Noise Ratio (SNR) constraints. This study aims to develop a deep learning model to automatically segment the rectum in a low-field MRI prostate image. 132, 3D images from ten patients were assembled. A 3D, U-Net model with the input matrix size 120×120×40 voxels was trained to detect and segment the rectum. The 3D U-Net can learn and integrate the relative information between adjacent MRI slices, which can enforce 3D patterns such as rectal wall smoothness and thus compensate for slice-to-slice variability in SNR and rectal boundary fuzziness. Contrast stretching, histogram equalization, and brightness enhancement were also investigated and applied to normalize intra- and inter- image intensity heterogeneity. Data augmentation methods such as elastic deformation, flipping, rotation, and scaling were also applied to reduce the risk of overfitting in model training. The model was trained and tested using a 4-fold cross-validation method with 3:1:2 split for training, validation, and testing. Study results show that the mean intersection over union score (IOUs) is 0.63 for the rectum on the testing dataset. Additionally, visual examination suggests that the displacement between the centroids of the ground truth and inferred volumetric segmentations is less than 3mm. Thus, this study demonstrates that (1) a 3D U-Net model can effectively segment the rectum on low-field MRI scans and (2) applying image processing and data augmentation can boost model performance.
Radiomics and deep transfer learning have been attracting broad research interest in developing and optimizing CAD schemes of medical images. However, these two technologies are typically applied in different studies using different image datasets. Advantages or potential limitations of applying these two technologies in CAD applications have not been well investigated. This study aims to compare and assess these two technologies in classifying breast lesions. A retrospective dataset including 2,778 digital mammograms is assembled in which 1,452 images depict malignant lesions and 1,326 images depict benign lesions. Two CAD schemes are developed to classify breast lesions. First, one scheme is applied to segment lesions and compute radiomics features, while another scheme applies a pre-trained residual net architecture (ResNet50) as a transfer learning model to extract automated features. Next, the same principal component algorithm (PCA) is used to process both initially computed radiomics and automated features to create optimal feature vectors by eliminating redundant features. Then, several support vector machine (SVM)-based classifiers are built using the optimized radiomics or automated features. Each SVM model is trained and tested using a 10-fold cross-validation method. Classification performance is evaluated using area under ROC curve (AUC). Two SVMs trained using radiomics and automated features yield AUC of 0.77±0.02 and 0.85±0.02, respectively. In addition, SVM trained using the fused radiomics and automated features does not yield significantly higher AUC. This study indicates that (1) using deep transfer learning yields higher classification performance, and (2) radiomics and automated features contain highly correlated information in lesion classification.
Computer-aided detection and/or diagnosis (CAD) schemes typically include machine learning classifiers trained using handcrafted features. The objective of this study is to investigate the feasibility of identifying and applying a new quantitative imaging marker to predict survival of gastric cancer patients. A retrospective dataset including CT images of 403 patients is assembled. Among them, 162 patients have more than 5-year survival. A CAD scheme is applied to segment gastric tumors depicted in multiple CT image slices. After gray-level normalization of each segmented tumor region to reduce image value fluctuation, we used a special feature selection library of a publicly available Pyradiomics software to compute 103 features. To identify an optimal approach to predict patient survival, we investigate two logistic regression model (LRM) generated imaging markers. The first one fuses image features computed from one CT slice and the second one fuses the weighted average image features computed from multiple CT slices. Two LRMs are trained and tested using a leave-one-case-out cross-validation method. Using the LRM-generated prediction scores, receiving operating characteristics (ROC) curves are computed and the area under ROC curve (AUC) is used as index to evaluate performance in predicting patients’ survival. Study results show that the case prediction-based AUC values are 0.70 and 0.72 for two LRM-generated image markers fused with image features computed from a single CT slide and multiple CT slices, respectively. This study demonstrates that (1) radiomics features computed from CT images carry valuable discriminatory information to predict survival of gastric cancer patients and (2) fusion of quasi-3D image features yields higher prediction accuracy than using simple 2D image features.
Computer-Aided Diagnosis (CAD) schemes used to classify suspicious breast lesions typically include machine learning classifiers that are trained using features computed from either the segmented lesions or fixed regions of interest (ROIs) covering the lesions. Both methods have advantages and disadvantages. In this study, we investigate a new approach to train a machine learning classifier that fuses image features computed from both the segmented lesions and the fixed ROIs. We assembled a dataset with 2,000 mammograms. Based on lesion center, a ROI is extracted from each image. Among them, 1,000 ROIs depict verified malignant lesions and rest include benign lesions. An adaptive multilayer region growing algorithm is applied to segment suspicious lesions. Several sets of statistical features, texture features based on GLRLM, GLDM and GLCM, Wavelet transformed features and shape-based features are computed from the original ROI and segmented lesion, respectively. Three support vector machines (SVM) are trained using features computed from original ROIs, segmented lesions, and fusion of both, respectively, using a 10-fold cross-validation method embedded with a feature reduction method, namely a random projection algorithm. By applying the area under the ROC curve (AUC) as an evaluation index, our study results reveal no significant difference between AUC values computed using classification scores generated by two SVMs trained with features computed from original ROIs or segmented lesions. However, utilizing the fused features, AUC of SVM increases more than 10% (p<0.05). This study demonstrates that image features computed using the segmented lesions and the fixed ROIs contain complementary discriminatory information. Thus, fusing these features can significantly improve CAD performance.
Computer-aided detection and/or diagnosis schemes typically include machine learning classifiers trained using either handcrafted features or deep learning model-generated automated features. The objective of this study is to investigate a new method to effectively select optimal feature vectors from an extremely large automated feature pool and the feasibility of improving the performance of a machine learning classifier trained using the fused handcrafted and automated feature sets. We assembled a retrospective image dataset involving 1,535 mammograms in which 740 and 795 images depict malignant and benign lesions, respectively. For each image, a region of interest (ROI) around the center of the lesion is extracted. First, 40 handcrafted features are computed. Two automated feature set are extracted from a VGG16 network pretrained using the ImageNet dataset. The first automated feature set is extracted using pseudo color images created by stacking the original image, a bilateral filtered image, and a histogram equalized image. The second automated feature set is created by stacking the original image in three channels. Two fused feature sets are then created by fusing the handcrafted feature set with each automated feature set, respectively. Five linear support vector machines are then trained using a 10- fold cross-validation method. The classification accuracy and AUC of the SVMs trained using the fused feature sets performs significantly better than using handcrafted or automated features alone (p<0.05). Study results demonstrate that handcrafted and automated features contain complimentary information so that fusion together create classifiers with improved performance in classifying breast lesions as malignant or benign.
The purpose of this study is to develop a machine learning model with the optimal features computed from mammograms to classify suspicious regions as benign and malignant. To this aim, we investigate the benefits of implementing a machine learning approach embedded with a random projection algorithm to generate an optimal feature vector and improve classification performance. A retrospective dataset involving 1,487 cases is used. Among them, 644 cases depict malignant lesions, while the rest 843 cases are benign. The locations of all suspicious regions have been annotated by radiologists before. A computer-aided detection scheme is applied to pre-process the images and compute an initial set of 181 features. Then, three support vector machine (SVM) models are built using the initial feature set and embedded with two feature regeneration methods, namely, principal component analysis and random projection algorithm, to reduce dimensionality of feature space and generate smaller optimal feature vectors. All SVM models are trained and tested using the leave-one-case-out cross-validation method to classify between malignant and benign cases. The data analysis results show that three SVM models yield the areas under ROC curves of AUC = 0.72±0.02, 0.79±0.01 and 0.84±0.018, respectively. Thus, this study demonstrates that applying a random projection algorithm enables to generate optimal feature vectors and significantly improve machine learning model (i.e., SVM) performance (p<0.02) to classify mammographic lesions. The similar approach can also been applied to help more effectively train and improve performance of machine learning models applying to other types of medical image applications.
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