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BACKGROUND: Saliency-based algorithms are able to explain the relationship between input image pixels and deep-learning model predictions. However, it may be difficult to assess the clinical value of the most important image features and the model predictions derived from the raw saliency map. This study proposes to enhance the interpretability of saliency-based deep learning model for survival classification of patients with gliomas, by extracting domain knowledge-based information from the raw saliency maps. MATERIALS AND METHODS: Our study includes presurgical T1-weighted (pre- and post-contrast), T2-weighted and T2-FLAIR MRIs of 147 glioma patients from the BraTs 2020 challenge dataset aligned to the SRI 24 anatomical atlas. Each image exam includes a segmentation mask and the information of overall survival (OS) from time of diagnosis (in days). This dataset was divided into training ([Formula: see text]) and validation ([Formula: see text]) datasets. The extent of surgical resection for all patients was gross total resection. We categorized the data into 42 short (mean [Formula: see text] days), 30 medium ([Formula: see text] days), and 46 long ([Formula: see text] days) survivors. A 3D convolutional neural network (CNN) trained on brain tumour MRI volumes classified all patients based on expected prognosis of either short-term, medium-term, or long-term survival. We extend the popular 2D Gradient-weighted Class Activation Mapping (Grad-CAM), for the generation of saliency map, to 3D and combined it with the anatomical atlas, to extract brain regions, brain volume and probability map that reveal domain knowledge-based information. RESULTS: For each OS class, a larger tumor volume was associated with a shorter OS. There were 10, 7 and 27 tumor locations in brain regions that uniquely associate with the short-term, medium-term, and long-term survival, respectively. Tumors located in the transverse temporal gyrus, fusiform, and palladium are associated with short, medium and long-term survival, respectively. The visual and textual information displayed during OS prediction highlights tumor location and the contribution of different brain regions to the prediction of OS. This algorithm design feature assists the physician in analyzing and understanding different model prediction stages. CONCLUSIONS: Domain knowledge-based information extracted from the saliency map can enhance the interpretability of deep learning models. Our findings show that tumors overlapping eloquent brain regions are associated with short patient survival.

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BACKGROUND: Lung region segmentation is an important stage of automated image-based approaches for the diagnosis of respiratory diseases. Manual methods executed by experts are considered the gold standard, but it is time consuming and the accuracy is dependent on radiologists' experience. Automated methods are relatively fast and reproducible with potential to facilitate physician interpretation of images. However, these benefits are possible only after overcoming several challenges. The traditional methods that are formulated as a three-stage segmentation demonstrate promising results on normal CT data but perform poorly in the presence of pathological features and variations in image quality attributes. The implementation of deep learning methods that can demonstrate superior performance over traditional methods is dependent on the quantity, quality, cost and the time it takes to generate training data. Thus, efficient and clinically relevant automated segmentation method is desired for the diagnosis of respiratory diseases. METHODS: We implement each of the three stages of traditional methods using deep learning methods trained on five different configurations of training data with ground truths obtained from the 3D Image Reconstruction for Comparison of Algorithm Database (3DIRCAD) and the Interstitial Lung Diseases (ILD) database. The data was augmented with the Lung Image Database Consortium (LIDC-IDRI) image collection and a realistic phantom. A convolutional neural network (CNN) at the preprocessing stage classifies the input into lung and none lung regions. The processing stage was implemented using a CNN-based U-net while the postprocessing stage utilize another U-net and CNN for contour refinement and filtering out false positives, respectively. RESULTS: The performance of the proposed method was evaluated on 1230 and 1100 CT slices from the 3DIRCAD and ILD databases. We investigate the performance of the proposed method on five configurations of training data and three configurations of the segmentation system; three-stage segmentation and three-stage segmentation without a CNN classifier and contrast enhancement, respectively. The Dice-score recorded by the proposed method range from 0.76 to 0.95. CONCLUSION: The clinical relevance and segmentation accuracy of deep learning models can improve though deep learning-based three-stage segmentation, image quality evaluation and enhancement as well as augmenting the training data with large volume of cheap and quality training data. We propose a new and novel deep learning-based method of contour refinement.

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Noise-based quality evaluation of MRI images is highly desired in noise-dominant environments. Current noise-based MRI quality evaluation methods have drawbacks which limit their effective performance. Traditional full-reference methods such as SNR and most of the model-based techniques cannot provide perceptual quality metrics required for accurate diagnosis, treatment and monitoring of diseases. Although techniques based on the Moran coefficients are perceptual quality metrics, they are full-reference methods and will be ineffective in applications where the reference image is not available. Furthermore, the predicted quality scores are difficult to interpret because their quality indices are not standardized. In this paper, we propose a new no-reference perceptual quality evaluation method for grayscale images such as MRI images. Our approach is formulated to mimic how humans perceive an image. It transforms noise level into a standardized perceptual quality score. Global Moran statistics is combined with local indicators of spatial autocorrelation in the form of local Moran statistics. Quality score is predicted from perceptually weighted combination of clustered and random pixels. Performance evaluation, comparative performance evaluation and validation by human observers, shows that the proposed method will be a useful tool in the evaluation of retrospectively acquired MRI images and the evaluation of noise reduction algorithms.

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Magnetic resonance imaging (MRI) system images are important components in the development of drugs because it can reveal the underlying pathology in diseases. Unfortunately, the processes of image acquisition, storage, transmission, processing, and analysis can influence image quality with the risk of compromising the reliability of MRI-based data. Therefore, it is necessary to monitor image quality throughout the different stages of the imaging workflow. This report describes a new approach to evaluate the quality of an MRI slice in multi-center clinical trials. The design philosophy assumes that an MRI slice, such as all natural images, possess statistical properties that can describe different levels of contrast degradation. A unique set of pixel configuration is assigned to each possible level of contrast-distorted MRI slice. Invocation of the central limit theorem results in two separate Gaussian distributions. The central limit theorem says that the mean and standard deviation of pixel configuration assigned to each possible level of contrast degradation will follow a normal distribution. The mean of each normal distribution corresponds to the mean and standard deviation of the underlying ideal image. Quality prediction processes for a test image can be summarized into four steps. The first step extracts local contrast feature image from the test image. The second step computes the mean and standard deviation of the feature image. The third step separately standardizes each normal distribution using the mean and standard deviation computed from the feature image. This gives two separate z-scores. The fourth step predicts the lightness contrast quality score and the texture contrast quality score from cumulative distribution function of the appropriate normal distribution. The proposed method was evaluated objectively on brain and cardiac MRI volume data using four different types and levels of degradation. The four types of degradation are Rician noise, circular blur, motion blur, and intensity nonuniformity also known as bias fields. Objective evaluation was validated using a proposed variation of difference of mean opinion scores. Results from performance evaluation show that the proposed method will be suitable to monitor and standardize image quality throughout the different stages of imaging workflow in large clinical trials. MATLAB implementation of the proposed objective quality evaluation method can be downloaded from (https://github.com/ezimic/Image-Quality-Evaluation).

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BACKGROUND: Multi-site neuroimaging offer several benefits and poses tough challenges in the drug development process. Although MRI protocol and clinical guidelines developed to address these challenges recommend the use of good quality images, reliable assessment of image quality is hampered by the several shortcomings of existing techniques. METHODS: Given a test image two feature images are extracted. They are grayscale and contrast feature images. Four binary images are generated by setting four different global thresholds on the feature images. Image quality is predicted by measuring the structural similarity between appropriate pairs of binary images. The lower and upper limits of the quality index are 0 and 1. Quality prediction is based on four quality attributes; luminance contrast, texture, texture contrast and lightness. RESULTS: Performance evaluation on test data from three multi-site clinical trials show good objective quality evaluation across MRI sequences, levels of distortion and quality attributes. Correlation with subjective evaluation by human observers is ≥ 0.6. CONCLUSION: The results are promising for the evaluation of MRI protocols, specifically the standardization of quality index, designed to overcome the challenges encountered in multi-site clinical trials.

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BACKGROUND: Rician noise, bias fields and blur are the common distortions that degrade MRI images during acquisition. Blur is unique in comparison to Rician noise and bias fields because it can be introduced into an image beyond the acquisition stage such as postacquisition processing and the manifestation of pathological conditions. Most current blur assessment algorithms are designed and validated on consumer electronics such as television, video and mobile appliances. The few algorithms dedicated to medical images either requires a reference image or incorporate manual approach. For these reasons it is difficult to compare quality measures from different images and images with different contents. Furthermore, they will not be suitable in environments where large volumes of images are processed. In this report we propose a new blind blur assessment method for different types of MRI images and for different applications including automated environments. METHODS: Two copies of the test image are generated. Edge map is extracted by separately convolving each copy of the test image with two parallel difference of Gaussian filters. At the start of the multiscale representation, the initial output of the filters are equal. In subsequent scales of the multiscale representation, each filter is tuned to different operating parameters over the same fixed range of Gaussian scales. The filters are termed low and high energy filters based on their characteristics to successively attenuate and highlight edges over the range of multiscale representation. Quality score is predicted from the distance between the normalized mean of the edge maps at the final output of the filters. RESULTS: The proposed method was evaluated on cardiac and brain MRI images. Performance evaluation shows that the quality index has very good correlation with human perception and will be suitable for application in routine clinical practice and clinical research.

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We describe a postacquisition, attribute-based quality assessment method for brain magnetic resonance imaging (MRI) images. It is based on the application of Bayes theory to the relationship between entropy and image quality attributes. The entropy feature image of a slice is segmented into low- and high-entropy regions. For each entropy region, there are three separate observations of contrast, standard deviation, and sharpness quality attributes. A quality index for a quality attribute is the posterior probability of an entropy region given any corresponding region in a feature image where quality attribute is observed. Prior belief in each entropy region is determined from normalized total clique potential (TCP) energy of the slice. For TCP below the predefined threshold, the prior probability for a region is determined by deviation of its percentage composition in the slice from a standard normal distribution built from 250 MRI volume data provided by Alzheimer's Disease Neuroimaging Initiative. For TCP above the threshold, the prior is computed using a mathematical model that describes the TCP-noise level relationship in brain MRI images. Our proposed method assesses the image quality of each entropy region and the global image. Experimental results demonstrate good correlation with subjective opinions of radiologists for different types and levels of quality distortions.