Purpose:
To present a review of most commonly used techniques to analyze dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI), discusses their strengths and weaknesses, and outlines recent ...clinical applications of findings from these approaches.
Methods:
DCE‐MRI allows for noninvasive quantitative analysis of contrast agent (CA) transient in soft tissues. Thus, it is an important and well‐established tool to reveal microvasculature and perfusion in various clinical applications. In the last three decades, a host of nonparametric and parametric models and methods have been developed in order to quantify the CA's perfusion into tissue and estimate perfusion‐related parameters (indexes) from signal‐ or concentration–time curves. These indexes are widely used in various clinical applications for the detection, characterization, and therapy monitoring of different diseases.
Results:
Promising theoretical findings and experimental results for the reviewed models and techniques in a variety of clinical applications suggest that DCE‐MRI is a clinically relevant imaging modality, which can be used for early diagnosis of different diseases, such as breast and prostate cancer, renal rejection, and liver tumors.
Conclusions:
Both nonparametric and parametric approaches for DCE‐MRI analysis possess the ability to quantify tissue perfusion.
This paper introduces a deep-learning based computer-aided diagnostic (CAD) system for the early detection of acute renal transplant rejection. For noninvasive detection of kidney rejection at an ...early stage, the proposed CAD system is based on the fusion of both imaging markers and clinical biomarkers. The former are derived from diffusion-weighted magnetic resonance imaging (DW-MRI) by estimating the apparent diffusion coefficients (ADC) representing the perfusion of the blood and the diffusion of the water inside the transplanted kidney. The clinical biomarkers, namely: creatinine clearance (CrCl) and serum plasma creatinine (SPCr), are integrated into the proposed CAD system as kidney functionality indexes to enhance its diagnostic performance. The ADC maps are estimated for a user-defined region of interest (ROI) that encompasses the whole kidney. The estimated ADCs are fused with the clinical biomarkers and the fused data is then used as an input to train and test a convolutional neural network (CNN) based classifier. The CAD system is tested on DW-MRI scans collected from 56 subjects from geographically diverse populations and different scanner types/image collection protocols. The overall accuracy of the proposed system is 92.9% with 93.3% sensitivity and 92.3% specificity in distinguishing non-rejected kidney transplants from rejected ones. These results demonstrate the potential of the proposed system for a reliable non-invasive diagnosis of renal transplant status for any DW-MRI scans, regardless of the geographical differences and/or imaging protocol.
To accurately segment pathological and healthy lungs for reliable computer-aided disease diagnostics, a stack of chest CT scans is modeled as a sample of a spatially inhomogeneous joint 3D ...Markov-Gibbs random field (MGRF) of voxel-wise lung and chest CT image signals (intensities). The proposed learnable MGRF integrates two visual appearance sub-models with an adaptive lung shape submodel. The first-order appearance submodel accounts for both the original CT image and its Gaussian scale space (GSS) filtered version to specify local and global signal properties, respectively. Each empirical marginal probability distribution of signals is closely approximated with a linear combination of discrete Gaussians (LCDG), containing two positive dominant and multiple sign-alternate subordinate DGs. The approximation is separated into two LCDGs to describe individually the lungs and their background, i.e., all other chest tissues. The second-order appearance submodel quantifies conditional pairwise intensity dependencies in the nearest voxel 26-neighborhood in both the original and GSS-filtered images. The shape submodel is built for a set of training data and is adapted during segmentation using both the lung and chest appearances. The accuracy of the proposed segmentation framework is quantitatively assessed using two public databases (ISBI VESSEL12 challenge and MICCAI LOLA11 challenge) and our own database with, respectively, 20, 55, and 30 CT images of various lung pathologies acquired with different scanners and protocols. Quantitative assessment of our framework in terms of Dice similarity coefficients, 95-percentile bidirectional Hausdorff distances, and percentage volume differences confirms the high accuracy of our model on both our database (98.4±1.0%, 2.2±1.0 mm, 0.42±0.10%) and the VESSEL12 database (99.0±0.5%, 2.1±1.6 mm, 0.39±0.20%), respectively. Similarly, the accuracy of our approach is further verified via a blind evaluation by the organizers of the LOLA11 competition, where an average overlap of 98.0% with the expert's segmentation is yielded on all 55 subjects with our framework being ranked first among all the state-of-the-art techniques compared.
The objective of this work is to develop a computer-aided diagnostic system for early diagnosis of prostate cancer. The presented system integrates both clinical biomarkers (prostate-specific ...antigen) and extracted features from diffusion-weighted magnetic resonance imaging collected at multiple b values. The presented system performs 3 major processing steps. First, prostate delineation using a hybrid approach that combines a level-set model with nonnegative matrix factorization. Second, estimation and normalization of diffusion parameters, which are the apparent diffusion coefficients of the delineated prostate volumes at different b values followed by refinement of those apparent diffusion coefficients using a generalized Gaussian Markov random field model. Then, construction of the cumulative distribution functions of the processed apparent diffusion coefficients at multiple b values. In parallel, a K-nearest neighbor classifier is employed to transform the prostate-specific antigen results into diagnostic probabilities. Finally, those prostate-specific antigen–based probabilities are integrated with the initial diagnostic probabilities obtained using stacked nonnegativity constraint sparse autoencoders that employ apparent diffusion coefficient–cumulative distribution functions for better diagnostic accuracy. Experiments conducted on 18 diffusion-weighted magnetic resonance imaging data sets achieved 94.4% diagnosis accuracy (sensitivity = 88.9% and specificity = 100%), which indicate the promising results of the presented computer-aided diagnostic system.
Objective: Early diagnosis of acute renal transplant rejection (ARTR) is critical for accurate treatment. Although the current gold standard, diagnostic technique is renal biopsy, it is not preferred ...due to its invasiveness, long recovery time (1-2 weeks), and potential for complications, e.g., bleeding and/or infection. Methods: This paper presents a computer-aided diagnostic (CAD) system for early ARTR detection using (3D + b-value) diffusion-weighted (DW) magnetic resonance imaging (MRI) data. The CAD process starts from kidney tissue segmentation with an evolving geometric (level-set-based) deformable model. The evolution is guided by a voxel-wise stochastic speed function, which follows from a joint kidney-background Markov-Gibbs random field model accounting for an adaptive kidney shape prior and on-going kidney-background visual appearances. A B-spline-based three-dimensional data alignment is employed to handle local deviations due to breathing and heart beating. Then, empirical cumulative distribution functions of apparent diffusion coefficients of the segmented DW-MRI at different b-values are collected as discriminatory transplant status features. Finally, a deep-learning-based classifier with stacked nonnegative constrained autoencoders is employed to distinguish between rejected and nonrejected renal transplants. Results: In our initial "leave-one-subject-out" experiment on 100 subjects, 97.0% of the subjects were correctly classified. The subsequent four-fold and ten-fold cross-validations gave the average accuracy of 96.0% and 94.0%, respectively. Conclusion: These results demonstrate the promise of this new CAD system to reliably diagnose renal transplant rejection. Significance: The technology presented here can significantly impact the quality of care of renal transplant patients since it has the potential to replace the gold standard in kidney diagnosis, biopsy.
Early diagnosis of transplanted kidney function requires precise Kidney segmentation from Dynamic Contrast-Enhanced Magnetic Resonance Imaging images as a preliminary step. In this regard, this paper ...aims to propose an automated and accurate DCE-MRI kidney segmentation method integrating fuzzy c-means (FCM) clustering and Markov random field modeling into a level set formulation. The fuzzy memberships, kidney's shape prior model, and spatial interactions modeled using a second-order MRF guide the LS contour evolution towards the target kidney. Several experiments on real medical data of 45 subjects have shown that the proposed method can achieve high and consistent segmentation accuracy regardless of where the LS contour was initialized. It achieves an accuracy of 0.956 ± 0.019 in Dice similarity coefficient (DSC) and 1.15 ± 1.46 in 95% percentile of Hausdorff distance (HD95). Our quantitative comparisons confirm the superiority of the proposed method over several LS methods with an average improvement of more than 0.63 in terms of HD95. It also offers HD95 improvements of 9.62 and 3.94 over two deep neural networks based on the U-Net model. The accuracy improvements are experimentally found to be more profound on low-contrast images as well as DCE-MRI images with high noise levels.
A new technique for more accurate automatic segmentation of the kidney from its surrounding abdominal structures in diffusion-weighted magnetic resonance imaging (DW-MRI) is presented. This approach ...combines a new 3D probabilistic shape model of the kidney with a first-order appearance model and fourth-order spatial model of the diffusion-weighted signal intensity to guide the evolution of a 3D geometric deformable model. The probabilistic shape model was built from labeled training datasets to produce a spatially variant, independent random field of region labels. A Markov-Gibbs random field spatial model with up to fourth-order interactions was adequate to capture the inhomogeneity of renal tissues in the DW-MRI signal. A new analytical approach estimated the Gibbs potentials directly from the DW-MRI data to be segmented, in order that the segmentation procedure would be fully automatic. Finally, to better distinguish the kidney object from the surrounding tissues, marginal gray level distributions inside and outside of the deformable boundary were modeled with adaptive linear combinations of discrete Gaussians (first-order appearance model). The approach was tested on a cohort of 64 DW-MRI datasets with b-values ranging from 50 to 1000 s/mm2. The performance of the presented approach was evaluated using leave-one-subject-out cross validation and compared against three other well-known segmentation methods applied to the same DW-MRI data using the following evaluation metrics: 1) the Dice similarity coefficient (DSC); 2) the 95-percentile modified Hausdorff distance (MHD); and 3) the percentage kidney volume difference (PKVD). High performance of the new approach was confirmed by the high DSC (0.95±0.01), low MHD (3.9±0.76) mm, and low PKVD (9.5±2.2)% relative to manual segmentation by an MR expert (a board certified radiologist).
Purpose
Early assessment of renal allograft function post‐transplantation is crucial to minimize and control allograft rejection. Biopsy — the gold standard — is used only as a last resort due to its ...invasiveness, high cost, adverse events (e.g., bleeding, infection, etc.), and the time for reporting. To overcome these limitations, a renal computer‐assisted diagnostic (Renal‐CAD) system was developed to assess kidney transplant function.
Methods
The developed Renal‐CAD system integrates data collected from two image‐based sources and two clinical‐based sources to assess renal transplant function. The imaging sources were the apparent diffusion coefficients (ADCs) extracted from 47 diffusion‐weighted magnetic resonance imaging (DW‐MRI) scans at 11 different b‐values (b0, b50, b100, ..., b1000 s/mm2), and the transverse relaxation rate (R2*) extracted from 30 blood oxygen level‐dependent MRI (BOLD‐MRI) scans at 5 different echo times (TEs = 2, 7, 12, 17, and 22 ms). Serum creatinine (SCr) and creatinine clearance (CrCl) were the clinical sources for kidney function evaluation. The Renal‐CAD system initially performed kidney segmentation using the level‐set method, followed by estimation of the ADCs from DW‐MRIs and the R2* from BOLD‐MRIs. ADCs and R2* estimates from 30 subjects that have both types of scans were integrated with their associated SCr and CrCl. The integrated biomarkers were then used as our discriminatory features to train and test a deep learning‐based classifier, namely stacked autoencoders (SAEs) to differentiate non‐rejection (NR) from acute rejection (AR) renal transplants.
Results
Using a leave‐one‐subject‐out cross‐validation approach along with SAEs, the Renal‐CAD system demonstrated 93.3% accuracy, 90.0% sensitivity, and 95.0% specificity in differentiating AR from NR. Robustness of the Renal‐CAD system was also confirmed by the area under the curve value of 0.92. Using a stratified tenfold cross‐validation approach, the Renal‐CAD system demonstrated its reproducibility and robustness by a diagnostic accuracy of 86.7%, sensitivity of 80.0%, specificity of 90.0%, and AUC of 0.88.
Conclusion
The obtained results demonstrate the feasibility and efficacy of accurate, noninvasive identification of AR at an early stage using the Renal‐CAD system.
The evolution in imaging has had an increasing role in the diagnosis, staging and follow up of bladder cancer. Conventional cystoscopy is crucial in the diagnosis of bladder cancer. However, a ...cystoscopic procedure cannot always depict carcinoma in situ (CIS) or differentiate benign from malignant tumors prior to biopsy. This review will discuss the standard application, novel imaging modalities and their additive role in patients with bladder cancer. Staging can be performed with CT, but distinguishing between T1 and T2 BCa (bladder cancer) cannot be assessed. MRI can distinguish muscle-invasive from non-muscle-invasive tumors with accurate local staging. Vesical Imaging-Reporting and Data System (VI-RADS) score is a new diagnostic modality used for the prediction of tumor aggressiveness and therapeutic response. Bone scintigraphy is recommended in patients with muscle-invasive BCa with suspected bony metastases. CT shows low sensitivity for nodal staging; however, PET (Positron Emission Tomography)/CT is superior and highly recommended for restaging and determining therapeutic effect. PET/MRI is a new imaging technique in bladder cancer imaging and its role is promising. Texture analysis has shown significant steps in discriminating low-grade from high-grade bladder cancer. Radiomics could be a reliable method for quantitative assessment of the muscle invasion of bladder cancer.
Prostate cancer is a significant cause of morbidity and mortality in the USA. In this paper, we develop a computer-aided diagnostic (CAD) system for automated grade groups (GG) classification using ...digitized prostate biopsy specimens (PBSs). Our CAD system aims to firstly classify the Gleason pattern (GP), and then identifies the Gleason score (GS) and GG. The GP classification pipeline is based on a pyramidal deep learning system that utilizes three convolution neural networks (CNN) to produce both patch- and pixel-wise classifications. The analysis starts with sequential preprocessing steps that include a histogram equalization step to adjust intensity values, followed by a PBSs’ edge enhancement. The digitized PBSs are then divided into overlapping patches with the three sizes: 100 × 100 (CNNS), 150 × 150 (CNNM), and 200 × 200 (CNNL), pixels, and 75% overlap. Those three sizes of patches represent the three pyramidal levels. This pyramidal technique allows us to extract rich information, such as that the larger patches give more global information, while the small patches provide local details. After that, the patch-wise technique assigns each overlapped patch a label as GP categories (1 to 5). Then, the majority voting is the core approach for getting the pixel-wise classification that is used to get a single label for each overlapped pixel. The results after applying those techniques are three images of the same size as the original, and each pixel has a single label. We utilized the majority voting technique again on those three images to obtain only one. The proposed framework is trained, validated, and tested on 608 whole slide images (WSIs) of the digitized PBSs. The overall diagnostic accuracy is evaluated using several metrics: precision, recall, F1-score, accuracy, macro-averaged, and weighted-averaged. The (CNNL) has the best accuracy results for patch classification among the three CNNs, and its classification accuracy is 0.76. The macro-averaged and weighted-average metrics are found to be around 0.70–0.77. For GG, our CAD results are about 80% for precision, and between 60% to 80% for recall and F1-score, respectively. Also, it is around 94% for accuracy and NPV. To highlight our CAD systems’ results, we used the standard ResNet50 and VGG-16 to compare our CNN’s patch-wise classification results. As well, we compared the GG’s results with that of the previous work.
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