Jennifer Steeden

Olivier Jaubert, Javier Montalt-Tordera, James Brown et al.

Purpose: Real-time monitoring of cardiac output (CO) requires low latency reconstruction and segmentation of real-time phase contrast MR (PCMR), which has previously been difficult to perform. Here we propose a deep learning framework for 'Flow Reconstruction and Segmentation for low latency Cardiac Output monitoring' (FReSCO). Methods: Deep artifact suppression and segmentation U-Nets were independently trained. Breath hold spiral PCMR data (n=516) was synthetically undersampled using a variable density spiral sampling pattern and gridded to create aliased data for training of the artifact suppression U-net. A subset of the data (n=96) was segmented and used to train the segmentation U-net. Real-time spiral PCMR was prospectively acquired and then reconstructed and segmented using the trained models (FReSCO) at low latency at the scanner in 10 healthy subjects during rest, exercise and recovery periods. CO obtained via FReSCO was compared to a reference rest CO and rest and exercise Compressed Sensing (CS) CO. Results: FReSCO was demonstrated prospectively at the scanner. Beat-to-beat heartrate, stroke volume and CO could be visualized with a mean latency of 622ms. No significant differences were noted when compared to reference at rest (Bias = -0.21+-0.50 L/min, p=0.246) or CS at peak exercise (Bias=0.12+-0.48 L/min, p=0.458). Conclusion: FReSCO was successfully demonstrated for real-time monitoring of CO during exercise and could provide a convenient tool for assessment of the hemodynamic response to a range of stressors.

Olivier Jaubert, Javier Montalt-Tordera, Daniel Knight et al.

PURPOSE: Interactive cardiac magnetic resonance imaging is used for fast scan planning and MR guided interventions. However, the requirement for real-time acquisition and near real-time visualization constrains the achievable spatio-temporal resolution. This study aims to improve interactive imaging resolution through optimization of undersampled spiral sampling and leveraging of deep learning for low-latency reconstruction (deep artifact suppression). METHODS: A variable density spiral trajectory was parametrized and optimized via HyperBand to provide the best candidate trajectory for rapid deep artifact suppression. Training data consisted of 692 breath-held CINEs. The developed interactive sequence was tested in simulations and prospectively in 13 subjects (10 for image evaluation, 2 during catheterization, 1 during exercise). In the prospective study, the optimized framework -HyperSLICE- was compared to conventional Cartesian real-time, and breath-hold CINE imaging in terms quantitative and qualitative image metrics. Statistical differences were tested using Friedman chi-squared tests with post-hoc Nemenyi test (p<0.05). RESULTS: In simulations the NRMSE, pSNR, SSIM and LAPE were all statistically significantly higher using optimized spiral compared to radial and uniform spiral sampling, particularly after scan plan changes (SSIM: 0.71 vs 0.45 and 0.43). Prospectively, HyperSLICE enabled a higher spatial and temporal resolution than conventional Cartesian real-time imaging. The pipeline was demonstrated in patients during catheter pull back showing sufficiently fast reconstruction for interactive imaging. CONCLUSION: HyperSLICE enables high spatial and temporal resolution interactive imaging. Optimizing the spiral sampling enabled better overall image quality and superior handling of image transitions compared to radial and uniform spiral trajectories.

Olivier Jaubert, Michele Pascale, Javier Montalt-Tordera et al.

Purpose: To develop and assess a deep learning (DL) pipeline to learn dynamic MR image reconstruction from publicly available natural videos (Inter4K). Materials and Methods: Learning was performed for a range of DL architectures (VarNet, 3D UNet, FastDVDNet) and corresponding sampling patterns (Cartesian, radial, spiral) either from true multi-coil cardiac MR data (N=692) or from pseudo-MR data simulated from Inter4K natural videos (N=692). Real-time undersampled dynamic MR images were reconstructed using DL networks trained with cardiac data and natural videos, and compressed sensing (CS). Differences were assessed in simulations (N=104 datasets) in terms of MSE, PSNR, and SSIM and prospectively for cardiac (short axis, four chambers, N=20) and speech (N=10) data in terms of subjective image quality ranking, SNR and Edge sharpness. Friedman Chi Square tests with post-hoc Nemenyi analysis were performed to assess statistical significance. Results: For all simulation metrics, DL networks trained with cardiac data outperformed DL networks trained with natural videos, which outperformed CS (p<0.05). However, in prospective experiments DL reconstructions using both training datasets were ranked similarly (and higher than CS) and presented no statistical differences in SNR and Edge Sharpness for most conditions. Additionally, high SSIM was measured between the DL methods with cardiac data and natural videos (SSIM>0.85). Conclusion: The developed pipeline enabled learning dynamic MR reconstruction from natural videos preserving DL reconstruction advantages such as high quality fast and ultra-fast reconstructions while overcoming some limitations (data scarcity or sharing). The natural video dataset, code and pre-trained networks are made readily available on github. Key Words: real-time; dynamic MRI; deep learning; image reconstruction; machine learning;

Michele Pascale, Vivek Muthurangu, Javier Montalt Tordera et al.

Three-dimensional (3D) imaging is popular in medical applications, however, anisotropic 3D volumes with thick, low-spatial-resolution slices are often acquired to reduce scan times. Deep learning (DL) offers a solution to recover high-resolution features through super-resolution reconstruction (SRR). Unfortunately, paired training data is unavailable in many 3D medical applications and therefore we propose a novel unpaired approach; CLADE (Cycle Loss Augmented Degradation Enhancement). CLADE uses a modified CycleGAN architecture with a cycle-consistent gradient mapping loss, to learn SRR of the low-resolution dimension, from disjoint patches of the high-resolution plane within the anisotropic 3D volume data itself. We show the feasibility of CLADE in abdominal MRI and abdominal CT and demonstrate significant improvements in CLADE image quality over low-resolution volumes and state-of-the-art self-supervised SRR; SMORE (Synthetic Multi-Orientation Resolution Enhancement). Quantitative PIQUE (qualitative perception-based image quality evaluator) scores and quantitative edge sharpness (ES - calculated as the maximum gradient of pixel intensities over a border of interest), showed superior performance for CLADE in both MRI and CT. Qualitatively CLADE had the best overall image quality and highest perceptual ES over the low-resolution volumes and SMORE. This paper demonstrates the potential of using CLADE for super-resolution reconstruction of anisotropic 3D medical imaging data without the need for paired 3D training data.

Julius Åkesson, Iulius Dragonu, Einar Heiberg et al.

Purpose: Real-time (RT) bSSFP MRI enables fast free-breathing cardiovascular imaging but requires 10-16 slices for functional assessment, resulting in prolonged scan times. Simultaneous multi-slice (SMS) imaging can reduce acquisition time but when combined with non-Cartesian trajectories, it relies on iterative reconstructions that preclude online use. This study investigates deep artifact suppression to facilitate rapid, online reconstruction of RT-SMS. Methods: A spiral bSSFP SMS RT sequence with two simultaneously acquired slices was implemented at 1.5 T. Reconstruction used slice separation in k-space, followed by deep artifact suppression in image space using a 3D U-Net. Ten healthy volunteers were imaged. RT-SMS image quality and reconstruction time were compared between deep artifact suppression and compressed sensing (CS) reconstructions. Left (LV) and right (RV) ventricular volumes at end diastole (EDV) and end systole (ESV) and LV mass (LVM) were compared between RT-SMS with deep artifact suppression and reference-standard breath-hold (BH) imaging. Results: The RT-SMS acquisition was ~13x faster than BH imaging (15 s vs 3 min 15 s). RT-SMS reconstruction using deep artifact suppression was ~50x faster than CS (30 s vs 24 min 55 s). Deep artifact suppression consistently outperformed CS in quantitative and qualitative image quality (p<0.001). Functional agreement between BH and RT-SMS with deep artifact suppression was good (LVEDV: -7.5 +/- 6.8 ml, LVESV: -0.9 +/- 4.2 ml, RVEDV: -6.4 +/- 8.4 ml, RVESV: 0.2 +/- 10.7 ml, LVM: -10.3 +/- 11.0 g). Conclusion: Online deep artifact suppression reconstruction for RT-SMS bSSFP CMR enables free-breathing short-axis coverage with a substantial reduction in acquisition and reconstruction time while maintaining diagnostic image quality.

Mark Wrobel, Michele Pascale, Tina Yao et al.

Background: Conventional cardiovascular magnetic resonance (CMR) in paediatric and congenital heart disease uses 2D, breath-hold, balanced steady state free precession (bSSFP) cine imaging for assessment of function and cardiac-gated, respiratory-navigated, static 3D bSSFP whole-heart imaging for anatomical assessment. Our aim is to concatenate a stack 2D free-breathing real-time cines and use Deep Learning (DL) to create an isotropic a fully segmented 3D cine dataset from these images. Methods: Four DL models were trained on open-source data that performed: a) Interslice contrast correction; b) Interslice respiratory motion correction; c) Super-resolution (slice direction); and d) Segmentation of right and left atria and ventricles (RA, LA, RV, and LV), thoracic aorta (Ao) and pulmonary arteries (PA). In 10 patients undergoing routine cardiovascular examination, our method was validated on prospectively acquired sagittal stacks of real-time cine images. Quantitative metrics (ventricular volumes and vessel diameters) and image quality of the 3D cines were compared to conventional breath hold cine and whole heart imaging. Results: All real-time data were successfully transformed into 3D cines with a total post-processing time of <1 min in all cases. There were no significant biases in any LV or RV metrics with reasonable limits of agreement and correlation. There is also reasonable agreement for all vessel diameters, although there was a small but significant overestimation of RPA diameter. Conclusion: We have demonstrated the potential of creating a 3D-cine data from concatenated 2D real-time cine images using a series of DL models. Our method has short acquisition and reconstruction times with fully segmented data being available within 2 minutes. The good agreement with conventional imaging suggests that our method could help to significantly speed up CMR in clinical practice.

Anirudh Raman, Olivier Jaubert, Mark Wrobel et al.

Purpose: To investigate whether synthetically generated fractal data can be used to train deep learning (DL) models for dynamic MRI reconstruction, thereby avoiding the privacy, licensing, and availability limitations associated with cardiac MR training datasets. Methods: A training dataset was generated using quaternion Julia fractals to produce 2D+time images. Multi-coil MRI acquisition was simulated to generate paired fully sampled and radially undersampled k-space data. A 3D UNet deep artefact suppression model was trained using these fractal data (F-DL) and compared with an identical model trained on cardiac MRI data (CMR-DL). Both models were evaluated on prospectively acquired radial real-time cardiac MRI from 10 patients. Reconstructions were compared against compressed sensing(CS) and low-rank deep image prior (LR-DIP). All reconstrctuions were ranked for image quality, while ventricular volumes and ejection fraction were compared with reference breath-hold cine MRI. Results: There was no significant difference in qualitative ranking between F-DL and CMR-DL (p=0.9), while both outperformed CS and LR-DIP (p<0.001). Ventricular volumes and function derived from F-DL were similar to CMR-DL, showing no significant bias and accptable limits of agreement compared to reference cine imaging. However, LR-DIP had a signifcant bias (p=0.016) and wider lmits of agreement. Conclusion: DL models trained using synthetic fractal data can reconstruct real-time cardiac MRI with image quality and clinical measurements comparable to models trained on true cardiac MRI data. Fractal training data provide an open, scalable alternative to clinical datasets and may enable development of more generalisable DL reconstruction models for dynamic MRI.