Purpose To develop and evaluate the feasibility of deep learning approaches for magnetic resonance (MR) imaging-based attenuation correction (AC) (termed deep MRAC) in brain positron emission tomography (PET)/MR imaging. Materials and Methods A PET/MR imaging AC pipeline was built by using a deep learning approach to generate pseudo computed tomographic (CT) scans from MR images. A deep convolutional auto-encoder network was trained to identify air, bone, and soft tissue in volumetric head MR images coregistered to CT data for training. A set of 30 retrospective three-dimensional T1-weighted head images was used to train the model, which was then evaluated in 10 patients by comparing the generated pseudo CT scan to an acquired CT scan. A prospective study was carried out for utilizing simultaneous PET/MR imaging for five subjects by using the proposed approach. Analysis of covariance and paired-sample t tests were used for statistical analysis to compare PET reconstruction error with deep MRAC and two existing MR imaging-based AC approaches with CT-based AC. Results Deep MRAC provides an accurate pseudo CT scan with a mean Dice coefficient of 0.971 ± 0.005 for air, 0.936 ± 0.011 for soft tissue, and 0.803 ± 0.021 for bone. Furthermore, deep MRAC provides good PET results, with average errors of less than 1% in most brain regions. Significantly lower PET reconstruction errors were realized with deep MRAC (-0.7% ± 1.1) compared with Dixon-based soft-tissue and air segmentation (-5.8% ± 3.1) and anatomic CT-based template registration (-4.8% ± 2.2). Conclusion The authors developed an automated approach that allows generation of discrete-valued pseudo CT scans (soft tissue, bone, and air) from a single high-spatial-resolution diagnostic-quality three-dimensional MR image and evaluated it in brain PET/MR imaging. This deep learning approach for MR imaging-based AC provided reduced PET reconstruction error relative to a CT-based standard within the brain compared with current MR imaging-based AC approaches. RSNA, 2017 Online supplemental material is available for this article.

Purpose: To describe and evaluate a new fully automated musculoskeletal tissue segmentation method using deep convolutional neural network (CNN) and three-dimensional (3D) simplex deformable modeling to improve the accuracy and efficiency of cartilage and bone segmentation within the knee joint. Methods: A fully automated segmentation pipeline was built by combining a semantic segmentation CNN and 3D simplex deformable modeling. A CNN technique called SegNet was applied as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification. The 3D simplex deformable modeling refined the output from SegNet to preserve the overall shape and maintain a desirable smooth surface for musculoskeletal structure. The fully automated segmentation method was tested using a publicly available knee image data set to compare with currently used state-of-the-art segmentation methods. The fully automated method was also evaluated on two different data sets, which include morphological and quantitative MR images with different tissue contrasts. Results: The proposed fully automated segmentation method provided good segmentation performance with segmentation accuracy superior to most of state-of-the-art methods in the publicly available knee image data set. The method also demonstrated versatile segmentation performance on both morphological and quantitative musculoskeletal MR images with different tissue contrasts and spatial resolutions. Conclusion: The study demonstrates that the combined CNN and 3D deformable modeling approach is useful for performing rapid and accurate cartilage and bone segmentation within the knee joint. The CNN has promising potential applications in musculoskeletal imaging.

Purpose To determine the feasibility of using a deep learning approach to detect cartilage lesions (including cartilage softening, fibrillation, fissuring, focal defects, diffuse thinning due to cartilage degeneration, and acute cartilage injury) within the knee joint on MR images. Materials and Methods A fully automated deep learning-based cartilage lesion detection system was developed by using segmentation and classification convolutional neural networks (CNNs). Fat-suppressed T2-weighted fast spin-echo MRI data sets of the knee of 175 patients with knee pain were retrospectively analyzed by using the deep learning method. The reference standard for training the CNN classification was the interpretation provided by a fellowship-trained musculoskeletal radiologist of the presence or absence of a cartilage lesion within 17 395 small image patches placed on the articular surfaces of the femur and tibia. Receiver operating curve (ROC) analysis and the κ statistic were used to assess diagnostic performance and intraobserver agreement for detecting cartilage lesions for two individual evaluations performed by the cartilage lesion detection system. Results The sensitivity and specificity of the cartilage lesion detection system at the optimal threshold according to the Youden index were 84.1% and 85.2%, respectively, for evaluation 1 and 80.5% and 87.9%, respectively, for evaluation 2. Areas under the ROC curve were 0.917 and 0.914 for evaluations 1 and 2, respectively, indicating high overall diagnostic accuracy for detecting cartilage lesions. There was good intraobserver agreement between the two individual evaluations, with a κ of 0.76. Conclusion This study demonstrated the feasibility of using a fully automated deep learning-based cartilage lesion detection system to evaluate the articular cartilage of the knee joint with high diagnostic performance and good intraobserver agreement for detecting cartilage degeneration and acute cartilage injury. © RSNA, 2018 Online supplemental material is available for this article .

The combined CNN, 3D fully connected CRF, and 3D deformable modeling approach was well-suited for performing rapid and accurate comprehensive tissue segmentation of the knee joint. The deep learning-based segmentation method has promising potential applications in musculoskeletal imaging.

Purpose: To develop and evaluate a novel deep learning-based image reconstruction approach called MANTIS (Model-Augmented Neural neTwork with Incoherent k-space Sampling) for efficient MR parameter mapping. Methods: MANTIS combines end-to-end convolutional neural network (CNN) mapping, incoherent k-space undersampling, and a physical model as a synergistic framework. The CNN mapping directly converts a series of undersampled images straight into MR parameter maps using supervised training. Signal model fidelity is enforced by adding a pathway between the undersampled k-space and estimated parameter maps to ensure that the parameter maps produced synthesized k-space consistent with the acquired undersampling measurements. The MANTIS framework was evaluated on the T 2 mapping of the knee at different acceleration rates and was compared with 2 other CNN mapping methods and conventional sparsity-based iterative reconstruction approaches. Global quantitative assessment and regional T 2 analysis for the cartilage and meniscus were performed to demonstrate the reconstruction performance of MANTIS. Results: MANTIS achieved high-quality T 2 mapping at both moderate (R = 5) and high (R = 8) acceleration rates. Compared to conventional reconstruction approaches that exploited image sparsity, MANTIS yielded lower errors (normalized root mean square error of 6.1% for R = 5 and 7.1% for R = 8) and higher similarity (structural similarity index of 86.2% at R = 5 and 82.1% at R = 8) to the reference in the T 2 estimation. MANTIS also achieved superior performance compared to direct CNN mapping and a 2-step CNN method. Conclusion: The MANTIS framework, with a combination of end-to-end CNN mapping, signal model-augmented data consistency, and incoherent k-space sampling, is a promising approach for efficient and robust estimation of quantitative MR parameters. K E Y W O R D S convolutional neural network, deep learning, image reconstruction, incoherence k-space sampling, model augmentation, model-based reconstruction, MR parameter mapping | 175 LIU et aL.

To investigate the feasibility of using a deep learning-based approach to detect an anterior cruciate ligament (ACL) tear within the knee joint at MRI by using arthroscopy as the reference standard. Materials and Methods: A fully automated deep learning-based diagnosis system was developed by using two deep convolutional neural networks (CNNs) to isolate the ACL on MR images followed by a classification CNN to detect structural abnormalities within the isolated ligament. With institutional review board approval, sagittal proton density-weighted and fat-suppressed T2-weighted fast spinecho MR images of the knee in 175 subjects with a full-thickness ACL tear (98 male subjects and 77 female subjects; average age, 27.5 years) and 175 subjects with an intact ACL (100 male subjects and 75 female subjects; average age, 39.4 years) were retrospectively analyzed by using the deep learning approach. Sensitivity and specificity of the ACL tear detection system and five clinical radiologists for detecting an ACL tear were determined by using arthroscopic results as the reference standard. Receiver operating characteristic (ROC) analysis and two-sided exact binomial tests were used to further assess diagnostic performance. Results: The sensitivity and specificity of the ACL tear detection system at the optimal threshold were 0.96 and 0.96, respectively. In comparison, the sensitivity of the clinical radiologists ranged between 0.96 and 0.98, while the specificity ranged between 0.90 and 0.98. There was no statistically significant difference in diagnostic performance between the ACL tear detection system and clinical radiologists at P < .05. The area under the ROC curve for the ACL tear detection system was 0.98, indicating high overall diagnostic accuracy. Conclusion: There was no significant difference between the diagnostic performance of the ACL tear detection system and clinical radiologists for determining the presence or absence of an ACL tear at MRI.

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexibl representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplifie treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed ∼200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure.

Multicomponent T2 parameters of the articular cartilage of the human knee joint can be measured at 3.0T using mcDESPOT and show depth-dependent and regional-dependent variations.