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Applying Deep Learning to Accelerated Clinical Brain Magnetic Resonance Imaging for Multiple Sclerosis.

ABSTRACT: Background: Magnetic resonance (MR) scans are routine clinical procedures for monitoring people with multiple sclerosis (PwMS). Patient discomfort, timely scheduling, and financial burden motivate the need to accelerate MR scan time. We examined the clinical application of a deep learning (DL) model in restoring the image quality of accelerated routine clinical brain MR scans for PwMS. Methods: We acquired fast 3D T1w BRAVO and fast 3D T2w FLAIR MRI sequences (half the phase encodes and half the number of slices) in parallel to conventional parameters. Using a subset of the scans, we trained a DL model to generate images from fast scans with quality similar to the conventional scans and then applied the model to the remaining scans. We calculated clinically relevant T1w volumetrics (normalized whole brain, thalamic, gray matter, and white matter volume) for all scans and T2 lesion volume in a sub-analysis. We performed paired t-tests comparing conventional, fast, and fast with DL for these volumetrics, and fit repeated measures mixed-effects models to test for differences in correlations between volumetrics and clinically relevant patient-reported outcomes (PRO). Results: We found statistically significant but small differences between conventional and fast scans with DL for all T1w volumetrics. There was no difference in the extent to which the key T1w volumetrics correlated with clinically relevant PROs of MS symptom burden and neurological disability. Conclusion: A deep learning model that improves the image quality of the accelerated routine clinical brain MR scans has the potential to inform clinically relevant outcomes in MS.

SUBMITTER: Mani A

PROVIDER: S-EPMC8504490 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMultiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) are the two mimic autoimmune diseases of the central nervous system, which are rare in East Asia. Quantitative detection of contrast-enhancing lesions (CELs) on contrast-enhancing T1-weighted magnetic resonance (MR) images is of great significance for assessing the disease activity of MS and NMOSD. However, it is challenging to develop automatic segmentation algorithms due to the lack of data. In this work, we present an automatic segmentation model of CELs based on Fully Convolutional with Attention DenseNet (FCA-DenseNet) and transfer learning strategy to address the challenge of CEL quantification in small-scale datasets.MethodsA transfer learning approach was employed in this study, whereby pretraining was conducted using 77 MS subjects from the open access datasets (MICCAI 2016, MICCAI 2017, ISBI 2015) for white matter hyperintensity segmentation, followed by fine-tuning using 24 MS and NMOSD subjects from the local dataset for CEL segmentation. The proposed FCA-DenseNet combined the Fully Convolutional DenseNet and Convolutional Block Attention Module in order to improve the learning capability. A 2.5D data slicing strategy was used to process complex 3D MR images. U-Net, ResUNet, TransUNet, and Attention-UNet are used as comparison models to FCA-DenseNet. Dice similarity coefficient (DSC), positive predictive value (PPV), true positive rate (TPR), and volume difference (VD) are used as evaluation metrics to evaluate the performances of different models.ResultsFCA-DenseNet outperforms all other models in terms of all evaluation metrics, with a DSC of 0.661±0.187, PPV of 0.719±0.201, TPR of 0.680±0.254, and VD of 0.388±0.334. Transfer learning strategy has achieved success in building segmentation models on a small-scale local dataset where traditional deep learning approaches fail to train effectively.ConclusionsThe improved FCA-DenseNet, combined with transfer learning strategy and 2.5D data slicing strategy, has successfully addressed the challenges in constructing deep learning models on small-scale datasets, making it conducive to clinical quantification of brain CELs and diagnosis of MS and NMOSD.

Project description:BackgroundMultiple linear stapler firings during double stapling technique (DST) after laparoscopic low anterior resection (LAR) are associated with an increased risk of anastomotic leakage (AL). However, it is difficult to predict preoperatively the need for multiple linear stapler cartridges during DST anastomosis.AimTo develop a deep learning model to predict multiple firings during DST anastomosis based on pelvic magnetic resonance imaging (MRI).MethodsWe collected 9476 MR images from 328 mid-low rectal cancer patients undergoing LAR with DST anastomosis, which were randomly divided into a training set (n = 260) and testing set (n = 68). Binary logistic regression was adopted to create a clinical model using six factors. The sequence of fast spin-echo T2-weighted MRI of the entire pelvis was segmented and analyzed. Pure-image and clinical-image integrated deep learning models were constructed using the mask region-based convolutional neural network segmentation tool and three-dimensional convolutional networks. Sensitivity, specificity, accuracy, positive predictive value (PPV), and area under the receiver operating characteristic curve (AUC) was calculated for each model.ResultsThe prevalence of ≥ 3 linear stapler cartridges was 17.7% (58/328). The prevalence of AL was statistically significantly higher in patients with ≥ 3 cartridges compared to those with ≤ 2 cartridges (25.0% vs 11.8%, P = 0.018). Preoperative carcinoembryonic antigen level > 5 ng/mL (OR = 2.11, 95%CI 1.08-4.12, P = 0.028) and tumor size ≥ 5 cm (OR = 3.57, 95%CI 1.61-7.89, P = 0.002) were recognized as independent risk factors for use of ≥ 3 linear stapler cartridges. Diagnostic performance was better with the integrated model (accuracy = 94.1%, PPV = 87.5%, and AUC = 0.88) compared with the clinical model (accuracy = 86.7%, PPV = 38.9%, and AUC = 0.72) and the image model (accuracy = 91.2%, PPV = 83.3%, and AUC = 0.81).ConclusionMRI-based deep learning model can predict the use of ≥ 3 linear stapler cartridges during DST anastomosis in laparoscopic LAR surgery. This model might help determine the best anastomosis strategy by avoiding DST when there is a high probability of the need for ≥ 3 linear stapler cartridges.

Project description:BackgroundMulti-echo chemical-shift-encoded magnetic resonance imaging (MRI) has been widely used for fat quantification and fat suppression in clinical liver examinations. Clinical liver water-fat imaging typically requires breath-hold acquisitions, with the free-breathing acquisition method being more desirable for patient comfort. However, the acquisition for free-breathing imaging could take up to several minutes. The purpose of this study is to accelerate four-dimensional free-breathing whole-liver water-fat MRI by jointly using high-dimensional deep dictionary learning and model-guided (MG) reconstruction.MethodsA high-dimensional model-guided deep dictionary learning (HMDDL) algorithm is proposed for the acceleration. The HMDDL combines the powers of the high-dimensional dictionary learning neural network (hdDLNN) and the chemical shift model. The neural network utilizes the prior information of the dynamic multi-echo data in spatial respiratory motion, and echo dimensions to exploit the features of images. The chemical shift model is used to guide the reconstruction of field maps, R2∗ maps, water images, and fat images. Data acquired from ten healthy subjects and ten subjects with clinically diagnosed nonalcoholic fatty liver disease (NAFLD) were selected for training. Data acquired from one healthy subject and two NAFLD subjects were selected for validation. Data acquired from five healthy subjects and five NAFLD subjects were selected for testing. A three-dimensional (3D) blipped golden-angle stack-of-stars multi-gradient-echo pulse sequence was designed to accelerate the data acquisition. The retrospectively undersampled data were used for training, and the prospectively undersampled data were used for testing. The performance of the HMDDL was evaluated in comparison with the compressed sensing-based water-fat separation (CS-WF) algorithm and a parallel non-Cartesian recurrent neural network (PNCRNN) algorithm.ResultsFour-dimensional water-fat images with ten motion states for whole-liver are demonstrated at several R values. In comparison with the CS-WF and PNCRNN, the HMDDL improved the mean peak signal-to-noise ratio (PSNR) of images by 9.93 and 2.20 dB, respectively, and improved the mean structure similarity (SSIM) of images by 0.058 and 0.009, respectively, at R=10. The paired t-test shows that there was no significant difference between HMDDL and ground truth for proton-density fat fraction (PDFF) and R2∗ values at R up to 10.ConclusionsThe proposed HMDDL enables features of water images and fat images from the highly undersampled multi-echo data along spatial, respiratory motion, and echo dimensions, to improve the performance of accelerated four-dimensional (4D) free-breathing water-fat imaging.

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Applying Deep Learning to Accelerated Clinical Brain Magnetic Resonance Imaging for Multiple Sclerosis.

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