Magnetic resonance imaging (MRI) is well suited for Solid renal masses (SRMs) characterization (e.g., benign vs. malignant) due to its superior soft tissue contrast. Though renal mass detection and characterization using deep-learning (DL) methods have been extensively studied for computed tomography (CT) images, those same tasks are yet to be investigated on MRI images. SRMs need active surveillance as they consist of biologically diverse heterogeneous groups of benign or malignant masses. Among them, malignant clear cell renal carcinoma (ccRCC) is frequently aggressive. There are inter-observer and intra-observer differences in the assessment of SRMs by expert clinicians because of their experience and expertise. Therefore, it is essential to develop a machine learningbased noninvasive imaging diagnosis to distinguish SRMs as benign and malignant. Our retrospective study consisted of malignant (renal cell carcinoma- clear cell, papillary, and chromophobe) and benign (fat-poor angiomyolipoma-fpAML, oncocytomas) SRMs. We extracted first and second-order radiomics features from SRMs on T2W and T1W-CM MRI to train different machine learning (ML) models using the 5-fold cross-validation for benign vs malignant classification. The support vector machine (SVM) algorithm generated benign vs malignant classification accuracy of 90.00% with ROC-AUC of 76.19% on T2W MRI and the custom-designed multilayer perceptron model (MLP) model produced accuracy of 80.00% with ROC-AUC of 75.47% on T1W-CM MRI. Thus, ML-based radiomics features classification of SRMs extracted on MRI may be an alternative to biopsy using a non-invasive assessment of SRMs.
KEYWORDS: Kidney, Magnetic resonance imaging, Image segmentation, Cancer detection, Performance modeling, Tumor growth modeling, Data modeling, Deep learning
Due to the superior soft tissue contrast in magnetic resonance imaging (MRI), MRI may be well suited for renal mass characterization (e.g., benign vs. malignant). Though renal mass detection and characterization using deeplearning (DL) methods have been extensively studied for CT images, those same tasks are yet to be investigated on MR images. Existing algorithms for renal mass characterization require manual segmentation, therefore development of algorithms to localize and detect renal masses is important fully automatically. In this study, we developed a DL-based fully automated renal mass detection model on T2- weighted (T2W) images. In a cascaded approach, we initially segmented kidneys as a region-of-interest (ROI) using 2D U-Net model, then renal masses were detected on segmented kidneys using 2D U-Net convolutional neural network (CNN) model. We trained our model on randomly selected 80% of dataset using 5-fold cross-validation technique and evaluated on remaining 20% test cases for renal mass detection. Our T2W MRI dataset contained 108 patients with malignant (renal cell carcinoma- clear cell, papillary and chromophobe) and benign (fat poor angiomyolipoma-fpAML, oncocytomas) renal masses. The U-Net model for renal mass detection generated Dice similarity coefficient (DSC) of 90.00 ± 6.00 % (mean ± standard deviation). When localized kidneys evaluated on U-Net renal mass detection model yielded a sensitivity/recall, and specificity of 76.49% and 86.55%, respectively. Thus, our proposed fully automated cascaded approach has potential to be used as the first step in renal mass characterization study on T2W MRI images.
KEYWORDS: Kidney, Image segmentation, Magnetic resonance imaging, Cancer detection, Data modeling, Solids, Education and training, Tumor growth modeling, Tissues, 3D modeling
PurposeAccurate detection of small renal masses (SRM) is a fundamental step for automated classification of benign and malignant or indolent and aggressive renal tumors. Magnetic resonance image (MRI) may outperform computed tomography (CT) for SRM subtype differentiation due to improved tissue characterization, but is less explored compared to CT. The objective of this study is to autonomously detect SRM on contrast-enhanced magnetic resonance images (CE-MRI).ApproachIn this paper, we described a novel, fully automated methodology for accurate detection and localization of SRM on CE-MRI. We first determine the kidney boundaries using a U-Net convolutional neural network. We then search for SRM within the localized kidney regions using a mixture-of-experts ensemble model based on the U-Net architecture. Our dataset contained CE-MRI scans of 118 patients with different solid kidney tumor subtypes including renal cell carcinomas, oncocytomas, and fat-poor renal angiomyolipoma. We evaluated the proposed model on the entire CE-MRI dataset using 5-fold cross validation.ResultsThe developed algorithm reported a Dice similarity coefficient of 91.20 ± 5.41 % (mean ± standard deviation) for kidney segmentation from 118 volumes consisting of 25,025 slices. Our proposed ensemble model for SRM detection yielded a recall and precision of 86.2% and 83.3% on the entire CE-MRI dataset, respectively.ConclusionsWe described a deep-learning-based method for fully automated SRM detection using CE-MR images, which has not been studied previously. The results are clinically important as SRM localization is a pre-step for fully automated diagnosis of SRM subtypes.
KEYWORDS: Kidney, Image segmentation, Data modeling, Magnetic resonance imaging, 3D modeling, Performance modeling, Statistical modeling, 3D image processing, Tumor growth modeling, 3D acquisition
Purpose: Multiparametric magnetic resonance imaging (mp-MRI) is being investigated for kidney cancer because of better soft tissue contrast ability. The necessity of manual labels makes the development of supervised kidney segmentation algorithms challenging for each mp-MRI protocol. Here, we developed a transfer learning-based approach to improve kidney segmentation on a small dataset of five other mp-MRI sequences.
Approach: We proposed a fully automated two-dimensional (2D) attention U-Net model for kidney segmentation on T1 weighted-nephrographic phase contrast enhanced (CE)-MRI (T1W-NG) dataset (N = 108). The pretrained weights of T1W-NG kidney segmentation model transferred to five other distinct mp-MRI sequences model (T2W, T1W-in-phase (T1W-IP), T1W-out-of-phase (T1W-OP), T1W precontrast (T1W-PRE), and T1W-corticomedullary-CE (T1W-CM), N = 50) and fine-tuned by unfreezing the layers. The individual model performances were evaluated with and without transfer-learning fivefold cross-validation on average Dice similarity coefficient (DSC), absolute volume difference, Hausdorff distance (HD), and center-of-mass distance (CD) between algorithm generated and manually segmented kidneys.
Results: The developed 2D attention U-Net model for T1W-NG produced kidney segmentation DSC of 89.34 ± 5.31 % . Compared with randomly initialized weight models, the transfer learning-based models of five mp-MRI sequences showed average increase of 2.96% in DSC of kidney segmentation (p = 0.001 to 0.006). Specifically, the transfer-learning approach increased average DSC on T2W from 87.19% to 89.90%, T1W-IP from 83.64% to 85.42%, T1W-OP from 79.35% to 83.66%, T1W-PRE from 82.05% to 85.94%, and T1W-CM from 85.65% to 87.64%.
Conclusions: We demonstrate that a pretrained model for automated kidney segmentation of one mp-MRI sequence improved automated kidney segmentation on five other additional sequences.
KEYWORDS: Kidney, Image segmentation, Magnetic resonance imaging, 3D modeling, Data modeling, 3D image processing, Tumor growth modeling, Algorithm development, Tissues, Cancer
Multi-parametric magnetic resonance imaging (mp-MRI) is a promising tool for diagnosis of renal masses and may outperform computed tomography (CT) to differentiate between benign and malignant renal masses due to superior soft tissue contrast. Deep learning (DL)-based methods for kidney segmentation are under-explored in mp-MRI which consists of several pulse sequences, including primarily T2-weighted (T2W) and contrast-enhanced (CE) images. Multi-parametric MRI images have domain shift due to differences in acquisition systems and image protocols, leading to lack of generalizability of methods for image segmentation. To perform similar automated kidney segmentation on another mp- MRI sequence, the model needs a large dataset with manual segmentations to train a model from scratch, which is labor intensive and time consuming. In this paper, we first trained a DL-based method using 108 cases of labeled data to contour kidneys using T1 weighted-Nephrographic Phase CE-MRI (T1W-NG). We then applied a transfer learning approach to other mp-MRI images using pre-trained weights from the source domain, thus eliminating the need for large manually annotated datasets in target domain. The fully automated 2D U-Net for kidney segmentation in source domain containing total 108 3D images of T1W-NG, yielded Dice-similarity coefficient (DSC) of 0.91 ± 0.07 on test cases. The transfer learning of pretrained weights of T1W-NG model on the smaller target domain T2W dataset containing total 50 3D images for automated kidney segmentation generated DSC of 0.90 ± 0.06 (p<0.05), which was an improvement of 3.43% in DSC by compared to the without transfer learning approach (T2W-UNet model).
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