Machine learning is a technique for recognizing patterns that can be applied to medical images. Although it is a powerful tool that can help in rendering medical diagnoses, it can be misapplied. Machine learning typically begins with the machine learning algorithm system computing the image features that are believed to be of importance in making the prediction or diagnosis of interest. The machine learning algorithm system then identifies the best combination of these image features for classifying the image or computing some metric for the given image region. There are several methods that can be used, each with different strengths and weaknesses. There are open-source versions of most of these machine learning methods that make them easy to try and apply to images. Several metrics for measuring the performance of an algorithm exist; however, one must be aware of the possible associated pitfalls that can result in misleading metrics. More recently, deep learning has started to be used; this method has the benefit that it does not require image feature identification and calculation as a first step; rather, features are identified as part of the learning process. Machine learning has been used in medical imaging and will have a greater influence in the future. Those working in medical imaging must be aware of how machine learning works.

To develop and evaluate a fully automated algorithm for segmenting the abdomen from CT to quantify body composition. Materials and Methods: For this retrospective study, a convolutional neural network based on the U-Net architecture was trained to perform abdominal segmentation on a data set of 2430 two-dimensional CT examinations and was tested on 270 CT examinations. It was further tested on a separate data set of 2369 patients with hepatocellular carcinoma (HCC). CT examinations were performed between 1997 and 2015. The mean age of patients was 67 years; for male patients, it was 67 years (range, 29-94 years), and for female patients, it was 66 years (range, 31-97 years). Differences in segmentation performance were assessed by using twoway analysis of variance with Bonferroni correction. Results: Compared with reference segmentation, the model for this study achieved Dice scores (mean 6 standard deviation) of 0.98 6 0.03, 0.96 6 0.02, and 0.97 6 0.01 in the test set, and 0.94 6 0.05, 0.92 6 0.04, and 0.98 6 0.02 in the HCC data set, for the subcutaneous, muscle, and visceral adipose tissue compartments, respectively. Performance met or exceeded that of expert manual segmentation. Conclusion: Model performance met or exceeded the accuracy of expert manual segmentation of CT examinations for both the test data set and the hepatocellular carcinoma data set. The model generalized well to multiple levels of the abdomen and may be capable of fully automated quantification of body composition metrics in three-dimensional CT examinations.

Purpose:Imaging biomarker research focuses on discovering relationships between radiological features and histological findings. In glioblastoma patients, methylation of the O6-methylguanine methyltransferase (MGMT) gene promoter is positively correlated with an increased effectiveness of current standard of care. In this paper, the authors investigate texture features as potential imaging biomarkers for capturing the MGMT methylation status of glioblastoma multiforme (GBM) tumors when combined with supervised classification schemes.Methods:A retrospective study of 155 GBM patients with known MGMT methylation status was conducted. Co-occurrence and run length texture features were calculated, and both support vector machines (SVMs) and random forest classifiers were used to predict MGMT methylation status.Results:The best classification system (an SVM-based classifier) had a maximum area under the receiver-operating characteristic (ROC) curve of 0.85 (95% CI: 0.78–0.91) using four texture features (correlation, energy, entropy, and local intensity) originating from the T2-weighted images, yielding at the optimal threshold of the ROC curve, a sensitivity of 0.803 and a specificity of 0.813.Conclusions:Results show that supervised machine learning of MRI texture features can predict MGMT methylation status in preoperative GBM tumors, thus providing a new noninvasive imaging biomarker.

Predicting methylation of the O6-methylguanine methyltransferase (MGMT) gene status utilizing MRI imaging is of high importance since it is a predictor of response and prognosis in brain tumors. In this study, we compare three different residual deep neural network (ResNet) architectures to evaluate their ability in predicting MGMT methylation status without the need for a distinct tumor segmentation step. We found that the ResNet50 (50 layers) architecture was the best performing model, achieving an accuracy of 94.90% (+/- 3.92%) for the test set (classification of a slice as no tumor, methylated MGMT, or non-methylated). ResNet34 (34 layers) achieved 80.72% (+/- 13.61%) while ResNet18 (18 layers) accuracy was 76.75% (+/- 20.67%). ResNet50 performance was statistically significantly better than both ResNet18 and ResNet34 architectures (p < 0.001). We report a method that alleviates the need of extensive preprocessing and acts as a proof of concept that deep neural architectures can be used to predict molecular biomarkers from routine medical images.

Micro-CT is an important tool in biomedical research and preclinical applications that can provide visual inspection of and quantitative information about imaged small animals and biological samples such as vasculature specimens. Currently, micro-CT imaging uses projection data acquired at a large number (300 – 1000) of views, which can limit system throughput and potentially degrade image quality due to radiation-induced deformation or damage to the small animal or specimen. In this work, we have investigated low-dose micro-CT and its application to specimen imaging from substantially reduced projection data by using a recently developed algorithm, referred to as the adaptive-steepest-descent-projection-onto-convex-sets (ASD-POCS) algorithm, which reconstructs an image through minimizing the image total-variation and enforcing data constraints. To validate and evaluate the performance of the ASD-POCS algorithm, we carried out quantitative evaluation studies in a number of tasks of practical interest in imaging of specimens of real animal organs. The results show that the ASD-POCS algorithm can yield images with quality comparable to that obtained with existing algorithms, while using one-sixth to one quarter of the 361-view data currently used in typical micro-CT specimen imaging.

Purpose To test the utility of magnetization transfer imaging (MTI) in detection and monitoring the progression of renal fibrosis in mice with unilateral renal artery stenosis (RAS). Materials and Methods This prospective study was approved by the Institutional Animal Care and Use Committee. RAS (n=10) or sham surgery (n=5) was performed, and the stenotic and contralateral kidneys were studied longitudinally in-vivo at baseline and 2, 4 and 6 weeks post-surgery. Following a 16.4T MRI exam, magnetization transfer ratio (MTR) was measured as an index of fibrosis (guided by parameters selected in preliminary phantom studies). In addition, renal volume, perfusion, blood flow and oxygenation were assessed. Fibrosis was subsequently measured ex-vivo by histology and hydroxyproline assay. The Wilcoxon rank-sum or signed-rank test was used for statistical comparisons between or within groups, and Pearson’s and Spearman’s rank correlation to compare fibrosis measured in-vivo and ex-vivo. Results In the stenotic kidney, the median MTR showed progressive increases from baseline to 6 weeks post-surgery (by 13.7% [P=0.0006] and 21.3% [P=0.0005] in cortex and medulla, respectively), which were accompanied by a progressive loss in renal volume, perfusion, blood flow, and oxygenation. The 6-week MTR map showed good correlation with fibrosis measured ex-vivo (Pearson’s r=0.9038 and Spearman’s ρ=0.8107, P=0.0002 vs. trichrome staining; r=0.9540 and ρ=0.8821, P<0.0001 vs. Sirius red staining; r=0.8429 and ρ=0.7607, P=0.001 vs. hydroxyproline assay). Conclusion MT successfully measured and longitudinally monitored the progression of renal fibrosis in mice with unilateral RAS.

Deep learning techniques are being rapidly applied to medical imaging tasks—from organ and lesion segmentation to tissue and tumor classification. These techniques are becoming the leading algorithmic approaches to solve inherently difficult image processing tasks. Currently, the most critical requirement for successful implementation lies in the need for relatively large datasets that can be used for training the deep learning networks. Based on our initial studies of MR imaging examinations of the kidneys of patients affected by polycystic kidney disease (PKD), we have generated a unique database of imaging data and corresponding reference standard segmentations of polycystic kidneys. In the study of PKD, segmentation of the kidneys is needed in order to measure total kidney volume (TKV). Automated methods to segment the kidneys and measure TKV are needed to increase measurement throughput and alleviate the inherent variability of human-derived measurements. We hypothesize that deep learning techniques can be leveraged to perform fast, accurate, reproducible, and fully automated segmentation of polycystic kidneys. Here, we describe a fully automated approach for segmenting PKD kidneys within MR images that simulates a multi-observer approach in order to create an accurate and robust method for the task of segmentation and computation of TKV for PKD patients. A total of 2000 cases were used for training and validation, and 400 cases were used for testing. The multi-observer ensemble method had mean ± SD percent volume difference of 0.68 ± 2.2% compared with the reference standard segmentations. The complete framework performs fully automated segmentation at a level comparable with interobserver variability and could be considered as a replacement for the task of segmentation of PKD kidneys by a human.

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