Michele Pascale

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.

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.