Low Resolution Magnetic Resonance Images Research Articles

Inter-scanner super-resolution of 3D cine MRI using a transfer-learning network for MRgRT

Objective. Deep-learning networks for super-resolution (SR) reconstruction enhance the spatial-resolution of 3D magnetic resonance imaging (MRI) for MR-guided radiotherapy (MRgRT). However, variations between MRI scanners and patients impact the quality of SR for real-time 3D low-resolution (LR) cine MRI. In this study, we present a personalized super-resolution (psSR) network that incorporates transfer-learning to overcome the challenges in inter-scanner SR of 3D cine MRI. Approach: Development of the proposed psSR network comprises two-stages: (1) a cohort-specific SR (csSR) network using clinical patient datasets, and (2) a psSR network using transfer-learning to target datasets. The csSR network was developed by training on breath-hold and respiratory-gated high-resolution (HR) 3D MRIs and their k-space down-sampled LR MRIs from 53 thoracoabdominal patients scanned at 1.5 T. The psSR network was developed through transfer-learning to retrain the csSR network using a single breath-hold HR MRI and a corresponding 3D cine MRI from 5 healthy volunteers scanned at 0.55 T. Image quality was evaluated using the peak-signal-noise-ratio (PSNR) and the structure-similarity-index-measure (SSIM). The clinical feasibility was assessed by liver contouring on the psSR MRI using an auto-segmentation network and quantified using the dice-similarity-coefficient (DSC). Results. Mean PSNR and SSIM values of psSR MRIs were increased by 57.2% (13.8–21.7) and 94.7% (0.38–0.74) compared to cine MRIs, with the reference 0.55 T breath-hold HR MRI. In the contour evaluation, DSC was increased by 15% (0.79–0.91). Average time consumed for transfer-learning was 90 s, psSR was 4.51 ms per volume, and auto-segmentation was 210 ms, respectively. Significance. The proposed psSR reconstruction substantially increased image and segmentation quality of cine MRI in an average of 215 ms across the scanners and patients with less than 2 min of prerequisite transfer-learning. This approach would be effective in overcoming cohort- and scanner-dependency of deep-learning for MRgRT.

MRI super-resolution using similarity distance and multi-scale receptive field based feature fusion GAN and pre-trained slice interpolation network

Challenges arise in achieving high-resolution Magnetic Resonance Imaging (MRI) to improve disease diagnosis accuracy due to limitations in hardware, patient discomfort, long acquisition times, and high costs. While Convolutional Neural Networks (CNNs) have shown promising results in MRI super-resolution, they often don't look into the structural similarity and prior information available in consecutive MRI slices. By leveraging information from sequential slices, more robust features can be obtained, potentially leading to higher-quality MRI slices. We propose a multi-slice two-dimensional (2D) MRI super-resolution network that combines a Generative Adversarial Network (GAN) with feature fusion and a pre-trained slice interpolation network to achieve three-dimensional (3D) super-resolution. The proposed model requires consecutively acquired three low-resolution (LR) MRI slices along a specific axis, and achieves the reconstruction of the MRI slices in the remaining two axes. The network effectively enhances both in-plane and out-of-plane resolution along the sagittal axis while addressing computational and memory constraints in 3D super-resolution. The proposed generator has a in-plane and out-of-plane Attention (IOA) network that fuses both in-plane and out-plane features of MRI dynamically. In terms of out-of-plane attention, the network merges features by considering the similarity distance between features and for in-plane attention, the network employs a two-level pyramid structure with varying receptive fields to extract features at different scales, ensuring the inclusion of both global and local features. Subsequently, to achieve 3D MRI super-resolution, a pre-trained slice interpolation network is used that takes two consecutive super-resolved MRI slices to generate a new intermediate slice. To further enhance the network performance and perceptual quality, we introduce a feature up-sampling layer and a feature extraction block with Scaled Exponential Linear Unit (SeLU). Moreover, our super-resolution network incorporates VGG loss from a fine-tuned VGG-19 network to provide additional enhancement. Through experimental evaluations on the IXI dataset and BRATS dataset, using the peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM) and the number of training parameters, we demonstrate the superior performance of our method compared to the existing techniques. Also, the proposed model can be adapted or modified to achieve super-resolution for both 2D and 3D MRI data.

High-resolution 3T to 7T ADC map synthesis with a hybrid CNN-transformer model.

7 Tesla (7T) apparent diffusion coefficient (ADC) maps derived from diffusion-weighted imaging (DWI) demonstrate improved image quality and spatial resolution over 3 Tesla (3T) ADC maps. However, 7T magnetic resonance imaging (MRI) currently suffers from limited clinical unavailability, higher cost, and increased susceptibility to artifacts. To address these issues, we propose a hybrid CNN-transformer model to synthesize high-resolution 7T ADC maps from multimodal 3T MRI. The Vision CNN-Transformer (VCT), composed of both Vision Transformer (ViT) blocks and convolutional layers, is proposed to produce high-resolution synthetic 7T ADC maps from 3T ADC maps and 3T T1-weighted (T1w) MRI. ViT blocks enabled global image context while convolutional layers efficiently captured fine detail. The VCT model was validated on the publicly available Human Connectome Project Young Adult dataset, comprising 3T T1w, 3T DWI, and 7T DWI brain scans. The Diffusion Imaging in Python library was used to compute ADC maps from the DWI scans. A total of 171 patient cases were randomly divided into 130 training cases, 20 validation cases, and 21 test cases. The synthetic ADC maps were evaluated by comparing their similarity to the ground truth volumes with the following metrics: peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM), and mean squared error (MSE). In addition, RESULTS: The results are as follows: PSNR: 27.0±0.9dB, SSIM: 0.945±0.010, and MSE: 2.0E-3±0.4E-3. Both qualitative and quantitative results demonstrate that VCT performs favorably against other state-of-the-art methods. We have introduced various efficiency improvements, including the implementation of flash attention and training on 176×208 resolution images. These enhancements have resulted in the reduction of parameters and training time per epoch by 50% in comparison to ResViT. Specifically, the training time per epoch has been shortened from 7.67 min to 3.86 min. We propose a novel method to predict high-resolution 7T ADC maps from low-resolution 3T ADC maps and T1w MRI. Our predicted images demonstrate better spatial resolution and contrast compared to 3T MRI and prediction results made by ResViT and pix2pix. These high-quality synthetic 7T MR images could be beneficial for disease diagnosis and intervention, producing higher resolution and conformal contours, and as an intermediate step in generating synthetic CT for radiation therapy, especially when 7T MRI scanners are unavailable.

Utility of Adult-Based Discoid Lateral Meniscus Diagnostic Criteria in a Pediatric Population.

Commonly cited discoid lateral meniscus (DLM) imaging definitions are based on adult magnetic resonance imaging (MRI) measurements. This pathology commonly presents in pediatric populations; however, whether accepted adult measurements reliably apply to children and adolescents is unknown. This purposes of the study were to determine (1) the utility of applying adult-accepted MRI definitions of DLM to pediatric patients, (2) whether sex differences affect the applicability of the criteria, and (3) whether MRI magnet strength and/or tear presence affect MRI measurements for diagnosing DLM in pediatric patients. It was hypothesized that MRI criteria for DLM would be similar in adults and pediatric patients. Case series; Level of evidence, 4. A total of 100 consecutive MRIs from pediatric patients with DLM were evaluated, with 91 scans included. Two study authors independently reviewed the MRIs, evaluating meniscal height and width on sagittal and coronal images, "bow tie signs" on sagittal images, tibial sagittal and coronal width, and tear presence. For analysis, MRI magnet strength was dichotomized into high (>1.5 T) and low (<1.5 T) groups. The mean age of the patients at MRI evaluation was 12.3 ± 3.4 years; 51% of the patients were male, and 56% of the scans were of left knees. Included patients with DLM showed a mean of 3.68 bow tie signs, a sagittal total anterior to posterior meniscal width/tibial width ratio of 73%, a coronal meniscal width/tibial width ratio of 30%, and a coronal, transverse width of the lateral meniscus at the midportion of the meniscal body of 20.6 ± 7.7 mm. The MRI tesla strength of the images included in this study ranged from 0.3 to 3. It was determined that high- versus low-resolution MRI scans did not affect the inter- or intraobserver reliability of the MRI measurments (P > .05). However, several measurements showed improved intraclass correlation coefficients with increased tesla strength. This study confirms that pediatric patients with DLM, diagnosed by board-certified pediatric sports medicine orthopaedic surgeons, have measurements on MRI consistent with adult DLM diagnostic criteria. This finding held true regardless of sex or MRI tesla strength. Pediatric patients with DLM had >3 bow tie signs, >70% sagittal tibial plateau coverage, >14 mm coronal width, and >20% coronal tibial plateau coverage on MRI.

MFTN: Multi-Level Feature Transfer Network Based on MRI-Transformer for MR Image Super-resolution

Due to the unique environment and inherent properties of magnetic resonance imaging (MRI) instruments, MR images typically have lower resolution. Therefore, improving the resolution of MR images is beneficial for assisting doctors in diagnosing the condition. Currently, the existing MR image super-resolution (SR) methods still have the problem of insufficient detail reconstruction. To overcome this issue, this paper proposes a multi-level feature transfer network (MFTN) based on MRI-Transformer to realize SR of low-resolution MRI data. MFTN consists of a multi-scale feature reconstruction network (MFRN) and a multi-level feature extraction branch (MFEB). MFRN is constructed as a pyramid structure to gradually reconstruct image features at different scales by integrating the features obtained from MFEB, and MFEB is constructed to provide detail information at different scales for low resolution MR image SR reconstruction by constructing multiple MRI-Transformer modules. Each MRI-Transformer module is designed to learn the transfer features from the reference image by establishing feature correlations between the reference image and low-resolution MR image. In addition, a contrast learning constraint item is added to the loss function to enhance the texture details of the SR image. A large number of experiments show that our network can effectively reconstruct high-quality MR Images and achieves better performance compared to some state-of-the-art methods. The source code of this work will be released on GitHub.

High-resolution MRI synthesis using a data-driven framework with denoising diffusion probabilistic modeling

Objective. High-resolution magnetic resonance imaging (MRI) can enhance lesion diagnosis, prognosis, and delineation. However, gradient power and hardware limitations prohibit recording thin slices or sub-1 mm resolution. Furthermore, long scan time is not clinically acceptable. Conventional high-resolution images generated using statistical or analytical methods include the limitation of capturing complex, high-dimensional image data with intricate patterns and structures. This study aims to harness cutting-edge diffusion probabilistic deep learning techniques to create a framework for generating high-resolution MRI from low-resolution counterparts, improving the uncertainty of denoising diffusion probabilistic models (DDPM). Approach. DDPM includes two processes. The forward process employs a Markov chain to systematically introduce Gaussian noise to low-resolution MRI images. In the reverse process, a U-Net model is trained to denoise the forward process images and produce high-resolution images conditioned on the features of their low-resolution counterparts. The proposed framework was demonstrated using T2-weighted MRI images from institutional prostate patients and brain patients collected in the Brain Tumor Segmentation Challenge 2020 (BraTS2020). Main results. For the prostate dataset, the bicubic interpolation model (Bicubic), conditional generative-adversarial network (CGAN), and our proposed DDPM framework improved the noise quality measure from low-resolution images by 4.4%, 5.7%, and 12.8%, respectively. Our method enhanced the signal-to-noise ratios by 11.7%, surpassing Bicubic (9.8%) and CGAN (8.1%). In the BraTS2020 dataset, the proposed framework and Bicubic enhanced peak signal-to-noise ratio from resolution-degraded images by 9.1% and 5.8%. The multi-scale structural similarity indexes were 0.970 ± 0.019, 0.968 ± 0.022, and 0.967 ± 0.023 for the proposed method, CGAN, and Bicubic, respectively. Significance. This study explores a deep learning-based diffusion probabilistic framework for improving MR image resolution. Such a framework can be used to improve clinical workflow by obtaining high-resolution images without penalty of the long scan time. Future investigation will likely focus on prospectively testing the efficacy of this framework with different clinical indications.

SOFNet: Optical-flow based large-scale slice augmentation of brain MRI

Brain magnetic resonance imaging (MRI) data from multiple centers often exhibit variations in imaging conditions, such as the types of nuclear magnetic resonance instruments used and the presence of random noise. Additionally, discrepancies in the gap between MRI slices further complicate the usability of the data for advanced artificial intelligence (AI) analysis. Deep learning-based methods have emerged as practical solutions to address the challenge. However, existing research has largely overlooked the augmentation of brain MRI data, particularly when confronted with significant slice gaps, such as around 6 mm observed in our clinical brain MRI slices. In response to this research gap, we aim to develop novel approaches for augmenting brain MRI data, focusing on more significant slice gaps. To achieve this, we propose SOFNet, which utilizes the optical flow-based and encoder–decoder backbone. The primary objective of our model is to interpolate MRI slices while preserving feature consistency. Leveraging the optical flow method, which has exhibited exceptional performance compared to other super-resolution algorithms, our proposed approach has been evaluated on three distinct brain MRI datasets, explicitly addressing the gap between 4.2 mm and 6.0 mm. The experimental results highlight the significant enhancement in super-resolution quality achieved by SOFNet in generating adapted brain MRI data, surpassing other single-image super-resolution (SISR) methods in feature completion. To ensure the credibility of the interpolated brain MRI slices, we conducted experiments on three axes of MRI based on metrics such as peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). These experiments demonstrate the effectiveness of our approach in transforming low-resolution MRI data into clear and reliable brain MRIs, thereby enabling improved analysis using AI techniques.

Investigation of autosegmentation techniques on T2-weighted MRI for off-line dose reconstruction in MR-linac workflow for head and neck cancers.

In order to accurately accumulate delivered dose for head and neck cancer patients treated with the Adapt to Position workflow on the 1.5T magnetic resonance imaging (MRI)-linear accelerator (MR-linac), the low-resolution T2-weighted MRIs used for daily setup must be segmented to enable reconstruction of the delivered dose at each fraction. In this pilot study, we evaluate various autosegmentation methods for head and neck organs at risk (OARs) on on-board setup MRIs from the MR-linac for off-line reconstruction of delivered dose. Seven OARs (parotid glands, submandibular glands, mandible, spinal cord, and brainstem) were contoured on 43 images by seven observers each. Ground truth contours were generated using a simultaneous truth and performance level estimation (STAPLE) algorithm. Twenty total autosegmentation methods were evaluated in ADMIRE: 1-9) atlas-based autosegmentation using a population atlas library (PAL) of 5/10/15 patients with STAPLE, patch fusion (PF), random forest (RF) for label fusion; 10-19) autosegmentation using images from a patient's 1-4 prior fractions (individualized patient prior [IPP]) using STAPLE/PF/RF; 20) deep learning (DL) (3D ResUNet trained on 43 ground truth structure sets plus 45 contoured by one observer). Execution time was measured for each method. Autosegmented structures were compared to ground truth structures using the Dice similarity coefficient, mean surface distance (MSD), Hausdorff distance (HD), and Jaccard index (JI). For each metric and OAR, performance was compared to the inter-observer variability using Dunn's test with control. Methods were compared pairwise using the Steel-Dwass test for each metric pooled across all OARs. Further dosimetric analysis was performed on three high-performing autosegmentation methods (DL, IPP with RF and 4 fractions [IPP_RF_4], IPP with 1 fraction [IPP_1]), and one low-performing (PAL with STAPLE and 5 atlases [PAL_ST_5]). For five patients, delivered doses from clinical plans were recalculated on setup images with ground truth and autosegmented structure sets. Differences in maximum and mean dose to each structure between the ground truth and autosegmented structures were calculated and correlated with geometric metrics. DL and IPP methods performed best overall, all significantly outperforming inter-observer variability and with no significant difference between methods in pairwise comparison. PAL methods performed worst overall; most were not significantly different from the inter-observer variability or from each other. DL was the fastest method (33s per case) and PAL methods the slowest (3.7-13.8 min per case). Execution time increased with a number of prior fractions/atlases for IPP and PAL. For DL, IPP_1, and IPP_RF_4, the majority (95%) of dose differences were within±250cGy from ground truth, but outlier differences up to 785cGy occurred. Dose differences were much higher for PAL_ST_5, with outlier differences up to 1920cGy. Dose differences showed weak but significant correlations with all geometric metrics (R2 between 0.030 and 0.314). The autosegmentation methods offering the best combination of performance and execution time are DL and IPP_1. Dose reconstruction on on-board T2-weighted MRIs is feasible with autosegmented structures with minimal dosimetric variation from ground truth, but contours should be visually inspected prior to dose reconstruction in an end-to-end dose accumulation workflow.

PO-1691 Segmentation on low resolution magnetic resonance images for prostate radiotherapy

PO-1691 Segmentation on low resolution magnetic resonance images for prostate radiotherapy

Blind Super-Resolution of 3D MRI via Unsupervised Domain Transformation.

High-resolution medical images can be effectively used for clinical diagnosis. However, the acquisition of high-resolution images is difficult and often limited by medical instruments. Super-resolution (SR) methods provide a solution, where high-resolution (HR) images can be reconstructed from low-resolution (LR) ones. Most of existing deep neural networks for 3D SR medical images trained in a non-blind process, where LR images are directly degraded from HR data via a pre-determined downscale method. Such approaches rely heavily on the assumed degradation model, resulting in inevitable deviations in real clinical practice. Blind super-resolution, as a more attractive research line for this field, aims to generate HR images from LR inputs containing unknown degradation. Towards generalizing SR models for diverse types of degradation, we propose a robust blind SR of 3D medical images in an unsupervised manner with domain correction and upscaling treatment. First, a CycleGAN-based architecture is implemented to generate the LR data from the source domain to the target one for domain correction. Then, an upscaling network is learned via pre-determined HR-LR couples for reconstruction. The proposed framework is able to automatically learn noisy and blurry correction kernels for unpaired 3D SR magnetic resonance images (MRI). Our method achieves better and more robust performances in reconstruction of HR images from LR MRI with multiple unknown degradation processes, and show its superiority to other state-of-the-art supervised models and cycle-consistency based methods, especially in severe distortion cases.

Super-Resolution of Brain MRI via U-Net Architecture

This paper proposes a U-Net-based deep learning architecture for the task of super-resolution of lower resolution brain magnetic resonance images (MRI). The proposed system, called MRI-Net, is designed to learn the mapping between low-resolution and high-resolution MRI images. The system is trained using 50-800 2D MRI scans, depending on the architecture, and is evaluated using peak signal-to-noise ratio (PSNR) metrics on 10 randomly selected images. The proposed U-Net architecture outperforms current state-of-the-art networks in terms of PSNR when evaluated with a 3 x 3 resolution downsampling index. The system's ability to super-resolve MRI scans has the potential to enable physicians to detect pathologies better and perform a wider range of applications. The symmetrical downsampling pipeline used in this study allows for generically representing low-resolution MRI scans to highlight proof of concept for the U-Net-based approach. The system is implemented on PyTorch 1.9.0 with NVIDIA GPU processing to speed up training time. U-Net is a promising tool for medical applications in MRI, which can provide accurate and high-quality images for better diagnoses and treatment plans. The proposed approach has the potential to reduce the costs associated with high-resolution MRI scans by providing a solution for enhancing the image quality of low-resolution scans.

On the reliability of deep learning-based classification for Alzheimer's disease: Multi-cohorts, multi-vendors, multi-protocols, and head-to-head validation.

Structural changes in the brain due to Alzheimer’s disease dementia (ADD) can be observed through brain T1-weighted magnetic resonance imaging (MRI) images. Many ADD diagnostic studies using brain MRI images have been conducted with machine-learning and deep-learning models. Although reliability is a key in clinical application and applicability of low-resolution MRI (LRMRI) is a key to broad clinical application, both are not sufficiently studied in the deep-learning area. In this study, we developed a 2-dimensional convolutional neural network-based classification model by adopting several methods, such as using instance normalization layer, Mixup, and sharpness aware minimization. To train the model, MRI images from 2,765 cognitively normal individuals and 1,192 patients with ADD from the Samsung medical center cohort were exploited. To assess the reliability of our classification model, we designed external validation in multiple scenarios: (1) multi-cohort validation using four additional cohort datasets including more than 30 different centers in multiple countries, (2) multi-vendor validation using three different MRI vendor subgroups, (3) LRMRI image validation, and finally, (4) head-to-head validation using ten pairs of MRI images from ten individual subjects scanned in two different centers. For multi-cohort validation, we used the MRI images from 739 subjects from the Alzheimer’s Disease Neuroimaging Initiative cohort, 125 subjects from the Dementia Platform of Korea cohort, 234 subjects from the Premier cohort, and 139 subjects from the Gachon University Gil Medical Center. We further assessed classification performance across different vendors and protocols for each dataset. We achieved a mean AUC and classification accuracy of 0.9868 and 0.9482 in 5-fold cross-validation. In external validation, we obtained a comparable AUC of 0.9396 and classification accuracy of 0.8757 to other cross-validation studies in the ADNI cohorts. Furthermore, we observed the possibility of broad clinical application through LRMRI image validation by achieving a mean AUC and classification accuracy of 0.9404 and 0.8765 at cross-validation and AUC and classification accuracy of 0.8749 and 0.8281 at the ADNI cohort external validation.

Deep attention super-resolution of brain magnetic resonance images acquired under clinical protocols.

Vast quantities of Magnetic Resonance Images (MRI) are routinely acquired in clinical practice but, to speed up acquisition, these scans are typically of a quality that is sufficient for clinical diagnosis but sub-optimal for large-scale precision medicine, computational diagnostics, and large-scale neuroimaging collaborative research. Here, we present a critic-guided framework to upsample low-resolution (often 2D) MRI full scans to help overcome these limitations. We incorporate feature-importance and self-attention methods into our model to improve the interpretability of this study. We evaluate our framework on paired low- and high-resolution brain MRI structural full scans (i.e., T1-, T2-weighted, and FLAIR sequences are simultaneously input) obtained in clinical and research settings from scanners manufactured by Siemens, Phillips, and GE. We show that the upsampled MRIs are qualitatively faithful to the ground-truth high-quality scans (PSNR = 35.39; MAE = 3.78E−3; NMSE = 4.32E−10; SSIM = 0.9852; mean normal-appearing gray/white matter ratio intensity differences ranging from 0.0363 to 0.0784 for FLAIR, from 0.0010 to 0.0138 for T1-weighted and from 0.0156 to 0.074 for T2-weighted sequences). The automatic raw segmentation of tissues and lesions using the super-resolved images has fewer false positives and higher accuracy than those obtained from interpolated images in protocols represented with more than three sets in the training sample, making our approach a strong candidate for practical application in clinical and collaborative research.

Perceptual cGAN for MRI Super-resolution.

Capturing high-resolution magnetic resonance (MR) images is a time consuming process, which makes it unsuitable for medical emergencies and pediatric patients. Low-resolution MR imaging, by contrast, is faster than its high-resolution counterpart, but it compromises on fine details necessary for a more precise diagnosis. Super-resolution (SR), when applied to low-resolution MR images, can help increase their utility by synthetically generating high-resolution images with little additional time. In this paper, we present an SR technique for MR images that is based on generative adversarial networks (GANs), which have proven to be quite useful in producing sharp-looking details in SR. We introduce a conditional GAN with perceptual loss, which is conditioned upon the input low-resolution image, which improves the performance for isotropic and anisotropic MRI super-resolution. Clinical Relevance- MR image super-resolution has the potential for improving image acquisition speed to save the time of the clinicians, while guaranteeing high-quality images.

GCW-UNet segmentation of cardiac magnetic resonance images for evaluation of left atrial enlargement

Background and objectiveLeft atrial enlargement (LAE) is an anatomical variation of the left atrium and the result of the long-term increase of left atrial pressure. Most of the increase in stress or volume is due to potential cardiovascular disease. Studies have shown that LAE can independently predict the development of clinically significant cardiovascular disease and heart failure. If the left atrial volume is accurately measured, it will be an essential indicator of human health and an essential means for doctors to find patients' potential diseases. We can analyze the dynamic changes in the left atrial structure and analyze left atrial dilation. However, manual segmentation was inefficient and error-prone before the 3D reconstruction of the left atrium. In order to solve this problem, a convolution neural network (CNN) method based on cardiac magnetic resonance image (MRI) is proposed to automatically segment the left atrial region. MethodologyIn this paper, we have proposed and developed a novel U-Net with Gaussian blur and channel weight neural network (GCW-UNet) to automatically segment the left atrial region in the MRI of a patient with LAE. After Gaussian blur, different resolutions of the MRI are obtained. High-resolution MRI clearly shows the detailed features of the left atrium, while low-resolution MRI clearly shows the overall outline of the left atrium, which can solve the problem of more minor MRI features. Adaptive channel weights can enhance the atrial segmentation capability of the network. ResultsCompared with the state-of-the-art left atrial segmentation methods, our CNN-based technique results in the segmentation of the left atrium being closer to the manual segmentation by an experienced radiologist. On the test datasets, the mean Dice similarity coefficient reaches 93.57%. ConclusionFirstly, MRI has a small number of imaging artifacts, which results in low segmentation accuracy. Our method successfully solves the problem. Secondly, due to the high similarity between the background (the area outside the left atrium) and the foreground (the left atrium) in MRI, traditional neural networks misclassify the background as the foreground. Our GCW-Unit can address the imbalanced number of pixels between the foreground and background. Finally, after segmenting the left atrium in the MRI by GCW-Unit, we reconstructed the left atrium to model a three-dimensional heart of a patient suffering from LAE. Based on the different time frames of one heartbeat, we could present the dynamics of the left atrial structure during a cardiac cycle. This can better assist in the evaluation of LAE in heart patients.

Super-resolution reconstruction of magnetic resonance images based on multi-scale feature extraction Super-Resolution Convolution Neural Network

Background: Low-resolution magnetic resonance imaging (MRI) has high imaging speed, but the image details cannot meet the needs of clinical diagnosis. More and more researchers are interested in neural network-based reconstruction methods. How to effectively process the super-resolution reconstruction of the low-resolution images has become highly valuable in clinical applications. Methods: We introduced Super-Resolution Convolution Neural Network (SRCNN) into the reconstruction of magnetic resonance images. The SRCNN consists of three layers, the image feature extraction layer, the nonlinear mapping layer, and the reconstruction layer. For the feature extraction layer, a multi-scale feature extraction (MFE) method was used to extract the features in different scales by involving three different levels of views, which is superior to the original feature extraction in views with fixed size. Compared with the original feature extraction only in fixed size views, we used three different levels of views to extract the features of different scales. This MFE could also be combined with residual learning to improve the performance of MRI super-resolution reconstruction. The proposed network is an end-to-end architecture. Therefore, no manual intervention or multi-stage calculation is required in practical applications. The structure of the network is extremely simple by omitting the fully connected layers and the pooling layers from traditional Convolution Neural Network. Results and Conclusions: After comparative experiments, the effectiveness of the MFE SRCNN-based network in super-resolution reconstruction of MR images has been greatly improved. The performance is significantly improved in terms of evaluation indexes peak signal-to-noise ratio and structural similarity index measure, and the detail recovery of images is also improved.

Identification of Laminar Composition in Cerebral Cortex Using Low-Resolution Magnetic Resonance Images and Trust Region Optimization Algorithm.

Pathological changes in the cortical lamina can cause several mental disorders. Visualization of these changes in vivo would enhance their diagnostics. Recently a framework for visualizing cortical structures by magnetic resonance imaging (MRI) has emerged. This is based on mathematical modeling of multi-component T1 relaxation at the sub-voxel level. This work proposes a new approach for their estimation. The approach is validated using simulated data. Sixteen MRI experiments were carried out on healthy volunteers. A modified echo-planar imaging (EPI) sequence was used to acquire 105 individual volumes. Data simulating the images were created, serving as the ground truth. The model was fitted to the data using a modified Trust Region algorithm. In single voxel experiments, the estimation accuracy of the T1 relaxation times depended on the number of optimization starting points and the level of noise. A single starting point resulted in a mean percentage error (MPE) of 6.1%, while 100 starting points resulted in a perfect fit. The MPE was <5% for the signal-to-noise ratio (SNR) ≥ 38 dB. Concerning multiple voxel experiments, the MPE was <5% for all components. Estimation of T1 relaxation times can be achieved using the modified algorithm with MPE < 5%.

Synthesizing high-resolution magnetic resonance imaging using parallel cycle-consistent generative adversarial networks for fast magnetic resonance imaging.

The common practice in acquiring the magnetic resonance (MR) images is to obtain two-dimensional (2D) slices at coarse locations while keeping the high in-plane resolution in order to ensure enough body coverage while shortening the MR scan time. The aim of this study is to propose a novel method to generate HR MR images from low-resolution MR images along the longitudinal direction. In order to address the difficulty of collecting paired low- and high-resolution MR images in clinical settings and to gain the advantage of parallel cycle consistent generative adversarial networks (CycleGANs) in synthesizing realistic medical images, we developed a parallel CycleGANs based method using a self-supervised strategy. The proposed workflow consists of two parallely trained CycleGANs to independently predict the HR MR images in the two planes along the directions that are orthogonal to the longitudinal MR scan direction. Then, the final synthetic HR MR images are generated by fusing the two predicted images. MR images, including T1-weighted (T1), contrast enhanced T1-weighted (T1CE), T2-weighted (T2), and T2 Fluid Attenuated Inversion Recovery (FLAIR), of the multimodal brain tumor segmentation challenge 2020 (BraTS2020) dataset were processed to evaluate the proposed workflow along the cranial-caudal (CC), lateral, and anterior-posterior directions. Institutional collected MR images were also processed for evaluation of the proposed method. The performance of the proposed method was investigated via both qualitative and quantitative evaluations. Metrics of normalized mean absolute error (NMAE), peak signal-to-noise ratio (PSNR), edge keeping index (EKI), structural similarity index measurement (SSIM), information fidelity criterion (IFC), and visual information fidelity in pixel domain (VIFP) were calculated. It is shown that the proposed method can generate HR MR images visually indistinguishable from the ground truth in the investigations on the BraTS2020 dataset. In addition, the intensity profiles, difference images and SSIM maps can also confirm the feasibility of the proposed method for synthesizing HR MR images. Quantitative evaluations on the BraTS2020 dataset shows that the calculated metrics of synthetic HR MR images can all be enhanced for the T1, T1CE, T2, and FLAIR images. The enhancements in the numerical metrics over the low-resolution and bi-cubic interpolated MR images, as well as those genearted with a comparative deep learning method, are statistically significant. Qualitative evaluation of the synthetic HR MR images of the clinical collected dataset could also confirm the feasibility of the proposed method. The proposed method is feasible to synthesize HR MR images using self-supervised parallel CycleGANs, which can be expected to shorten MR acquisition time in clinical practices.

FA-GAN: Fused attentive generative adversarial networks for MRI image super-resolution.

High-resolution magnetic resonance images can provide fine-grained anatomical information, but acquiring such data requires a long scanning time. In this paper, a framework called the Fused Attentive Generative Adversarial Networks(FA-GAN) is proposed to generate the super- resolution MR image from low-resolution magnetic resonance images, which can reduce the scanning time effectively but with high resolution MR images. In the framework of the FA-GAN, the local fusion feature block, consisting of different three-pass networks by using different convolution kernels, is proposed to extract image features at different scales. And the global feature fusion module, including the channel attention module, the self-attention module, and the fusion operation, is designed to enhance the important features of the MR image. Moreover, the spectral normalization process is introduced to make the discriminator network stable. 40 sets of 3D magnetic resonance images (each set of images contains 256 slices) are used to train the network, and 10 sets of images are used to test the proposed method. The experimental results show that the PSNR and SSIM values of the super-resolution magnetic resonance image generated by the proposed FA-GAN method are higher than the state-of-the-art reconstruction methods.

Wide Weighted Attention Multi-Scale Network for Accurate MR Image Super-Resolution

High-quality magnetic resonance (MR) images afford more detailed information for reliable diagnoses and quantitative image analyses. Given low-resolution (LR) images, the deep convolutional neural network (CNN) has shown its promising ability for image super-resolution (SR). The LR MR images usually share some visual characteristics: structural textures of different sizes, edges with high correlation, and less informative background. However, multi-scale structural features are informative for image reconstruction, while the background is more smooth. Most previous CNN-based SR methods use a single receptive field and equally treat the spatial pixels (including the background). It neglects to sense the entire space and get diversified features from the input, which is critical for high-quality MR image SR. We propose a wide weighted attention multi-scale network ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{W}^{2}$ </tex-math></inline-formula> AMSN) for accurate MR image SR to address these problems. On the one hand, the features of varying sizes can be extracted by the wide multi-scale branches. On the other hand, we design a non-reduction attention mechanism to recalibrate feature responses adaptively. Such attention preserves continuous cross-channel interaction and focuses on more informative regions. Meanwhile, the learnable weighted factors fuse extracted features selectively. The encapsulated wide weighted attention multi-scale block ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{W}^{2}$ </tex-math></inline-formula> AMSB) is integrated through a recurrent framework and global attention mechanism. Extensive experiments and diversified ablation studies show the effectiveness of our proposed <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\text{W}^{2}$ </tex-math></inline-formula> AMSN, which surpasses state-of-the-art methods on most popular MR image SR benchmarks quantitatively and qualitatively. And our method still offers superior accuracy and adaptability on real MR images.