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Bayesian Uncertainty Estimation of Learned Variational MRI Reconstruction

Narnhofer, Dominik; Effland, Alexander; Kobler, Erich; Hammernik, Kerstin; Knoll, Florian; Pock, Thomas
Recent deep learning approaches focus on improving quantitative scores of dedicated benchmarks, and therefore only reduce the observation-related (aleatoric) uncertainty. However, the model-immanent (epistemic) uncertainty is less frequently systematically analyzed. In this work, we introduce a Bayesian variational framework to quantify the epistemic uncertainty. To this end, we solve the linear inverse problem of undersampled MRI reconstruction in a variational setting. The associated energy functional is composed of a data fidelity term and the total deep variation (TDV) as a learned parametric regularizer. To estimate the epistemic uncertainty we draw the parameters of the TDV regularizer from a multivariate Gaussian distribution, whose mean and covariance matrix are learned in a stochastic optimal control problem. In several numerical experiments, we demonstrate that our approach yields competitive results for undersampled MRI reconstruction. Moreover, we can accurately quantify the pixelwise epistemic uncertainty, which can serve radiologists as an additional resource to visualize reconstruction reliability.
PMID: 34506279
ISSN: 1558-254x
CID: 4998482

Results of the 2020 fastMRI Challenge for Machine Learning MR Image Reconstruction

Muckley, Matthew J; Riemenschneider, Bruno; Radmanesh, Alireza; Kim, Sunwoo; Jeong, Geunu; Ko, Jingyu; Jun, Yohan; Shin, Hyungseob; Hwang, Dosik; Mostapha, Mahmoud; Arberet, Simon; Nickel, Dominik; Ramzi, Zaccharie; Ciuciu, Philippe; Starck, Jean-Luc; Teuwen, Jonas; Karkalousos, Dimitrios; Zhang, Chaoping; Sriram, Anuroop; Huang, Zhengnan; Yakubova, Nafissa; Lui, Yvonne W; Knoll, Florian
Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.
PMID: 33929957
ISSN: 1558-254x
CID: 4853732

Artificial Intelligence for MR Image Reconstruction: An Overview for Clinicians

Lin, Dana J; Johnson, Patricia M; Knoll, Florian; Lui, Yvonne W
Artificial intelligence (AI) shows tremendous promise in the field of medical imaging, with recent breakthroughs applying deep-learning models for data acquisition, classification problems, segmentation, image synthesis, and image reconstruction. With an eye towards clinical applications, we summarize the active field of deep-learning-based MR image reconstruction. We review the basic concepts of how deep-learning algorithms aid in the transformation of raw k-space data to image data, and specifically examine accelerated imaging and artifact suppression. Recent efforts in these areas show that deep-learning-based algorithms can match and, in some cases, eclipse conventional reconstruction methods in terms of image quality and computational efficiency across a host of clinical imaging applications, including musculoskeletal, abdominal, cardiac, and brain imaging. This article is an introductory overview aimed at clinical radiologists with no experience in deep-learning-based MR image reconstruction and should enable them to understand the basic concepts and current clinical applications of this rapidly growing area of research across multiple organ systems.
PMID: 32048372
ISSN: 1522-2586
CID: 4304412

CG-SENSE revisited: Results from the first ISMRM reproducibility challenge

Maier, Oliver; Baete, Steven Hubert; Fyrdahl, Alexander; Hammernik, Kerstin; Harrevelt, Seb; Kasper, Lars; Karakuzu, Agah; Loecher, Michael; Patzig, Franz; Tian, Ye; Wang, Ke; Gallichan, Daniel; Uecker, Martin; Knoll, Florian
PURPOSE/OBJECTIVE:The aim of this work is to shed light on the issue of reproducibility in MR image reconstruction in the context of a challenge. Participants had to recreate the results of "Advances in sensitivity encoding with arbitrary k-space trajectories" by Pruessmann et al. METHODS: The task of the challenge was to reconstruct radially acquired multicoil k-space data (brain/heart) following the method in the original paper, reproducing its key figures. Results were compared to consolidated reference implementations created after the challenge, accounting for the two most common programming languages used in the submissions (Matlab/Python). RESULTS:Visually, differences between submissions were small. Pixel-wise differences originated from image orientation, assumed field-of-view, or resolution. The reference implementations were in good agreement, both visually and in terms of image similarity metrics. DISCUSSION AND CONCLUSION/CONCLUSIONS:While the description level of the published algorithm enabled participants to reproduce CG-SENSE in general, details of the implementation varied, for example, density compensation or Tikhonov regularization. Implicit assumptions about the data lead to further differences, emphasizing the importance of sufficient metadata accompanying open datasets. Defining reproducibility quantitatively turned out to be nontrivial for this image reconstruction challenge, in the absence of ground-truth results. Typical similarity measures like NMSE of SSIM were misled by image intensity scaling and outlier pixels. Thus, to facilitate reproducibility, researchers are encouraged to publish code and data alongside the original paper. Future methodological papers on MR image reconstruction might benefit from the consolidated reference implementations of CG-SENSE presented here, as a benchmark for methods comparison.
PMID: 33179826
ISSN: 1522-2594
CID: 4663022

Training a neural network for Gibbs and noise removal in diffusion MRI

Muckley, Matthew J; Ades-Aron, Benjamin; Papaioannou, Antonios; Lemberskiy, Gregory; Solomon, Eddy; Lui, Yvonne W; Sodickson, Daniel K; Fieremans, Els; Novikov, Dmitry S; Knoll, Florian
PURPOSE/OBJECTIVE:To develop and evaluate a neural network-based method for Gibbs artifact and noise removal. METHODS:A convolutional neural network (CNN) was designed for artifact removal in diffusion-weighted imaging data. Two implementations were considered: one for magnitude images and one for complex images. Both models were based on the same encoder-decoder structure and were trained by simulating MRI acquisitions on synthetic non-MRI images. RESULTS:Both machine learning methods were able to mitigate artifacts in diffusion-weighted images and diffusion parameter maps. The CNN for complex images was also able to reduce artifacts in partial Fourier acquisitions. CONCLUSIONS:The proposed CNNs extend the ability of artifact correction in diffusion MRI. The machine learning method described here can be applied on each imaging slice independently, allowing it to be used flexibly in clinical applications.
PMID: 32662910
ISSN: 1522-2594
CID: 4528102

Advancing machine learning for MR image reconstruction with an open competition: Overview of the 2019 fastMRI challenge

Knoll, Florian; Murrell, Tullie; Sriram, Anuroop; Yakubova, Nafissa; Zbontar, Jure; Rabbat, Michael; Defazio, Aaron; Muckley, Matthew J; Sodickson, Daniel K; Zitnick, C Lawrence; Recht, Michael P
PURPOSE/OBJECTIVE:To advance research in the field of machine learning for MR image reconstruction with an open challenge. METHODS:We provided participants with a dataset of raw k-space data from 1,594 consecutive clinical exams of the knee. The goal of the challenge was to reconstruct images from these data. In order to strike a balance between realistic data and a shallow learning curve for those not already familiar with MR image reconstruction, we ran multiple tracks for multi-coil and single-coil data. We performed a two-stage evaluation based on quantitative image metrics followed by evaluation by a panel of radiologists. The challenge ran from June to December of 2019. RESULTS:We received a total of 33 challenge submissions. All participants chose to submit results from supervised machine learning approaches. CONCLUSIONS:The challenge led to new developments in machine learning for image reconstruction, provided insight into the current state of the art in the field, and highlighted remaining hurdles for clinical adoption.
PMID: 32506658
ISSN: 1522-2594
CID: 4505052

Rapid mono and biexponential 3D-T1ρ mapping of knee cartilage using variational networks

Zibetti, Marcelo V W; Johnson, Patricia M; Sharafi, Azadeh; Hammernik, Kerstin; Knoll, Florian; Regatte, Ravinder R
In this study we use undersampled MRI acquisition methods to obtain accelerated 3D mono and biexponential spin-lattice relaxation time in the rotating frame (T1ρ) mapping of knee cartilage, reducing the usual long scan time. We compare the accelerated T1ρ maps obtained by deep learning-based variational network (VN) and compressed sensing (CS). Both methods were compared with spatial (S) and spatio-temporal (ST) filters. Complex-valued fitting was used for T1ρ parameters estimation. We tested with seven in vivo and six synthetic datasets, with acceleration factors (AF) from 2 to 10. Median normalized absolute deviation (MNAD), analysis of variance (ANOVA), and coefficient of variation (CV) were used for analysis. The methods CS-ST, VN-S, and VN-ST performed well for accelerating monoexponential T1ρ mapping, with MNAD around 5% for AF = 2, which increases almost linearly with the AF to an MNAD of 13% for AF = 8, with all methods. For biexponential mapping, the VN-ST was the best method starting with MNAD of 7.4% for AF = 2 and reaching MNAD of 13.1% for AF = 8. The VN was able to produce 3D-T1ρ mapping of knee cartilage with lower error than CS. The best results were obtained by VN-ST, improving CS-ST method by nearly 7.5%.
PMID: 33154515
ISSN: 2045-2322
CID: 4662942

Using Deep Learning to Accelerate Knee MRI at 3T: Results of an Interchangeability Study

Recht, Michael P; Zbontar, Jure; Sodickson, Daniel K; Knoll, Florian; Yakubova, Nafissa; Sriram, Anuroop; Murrell, Tullie; Defazio, Aaron; Rabbat, Michael; Rybak, Leon; Kline, Mitchell; Ciavarra, Gina; Alaia, Erin F; Samim, Mohammad; Walter, William R; Lin, Dana; Lui, Yvonne W; Muckley, Matthew; Huang, Zhengnan; Johnson, Patricia; Stern, Ruben; Zitnick, C Lawrence
OBJECTIVE:Deep Learning (DL) image reconstruction has the potential to disrupt the current state of MR imaging by significantly decreasing the time required for MR exams. Our goal was to use DL to accelerate MR imaging in order to allow a 5-minute comprehensive examination of the knee, without compromising image quality or diagnostic accuracy. METHODS:A DL model for image reconstruction using a variational network was optimized. The model was trained using dedicated multi-sequence training, in which a single reconstruction model was trained with data from multiple sequences with different contrast and orientations. Following training, data from 108 patients were retrospectively undersampled in a manner that would correspond with a net 3.49-fold acceleration of fully-sampled data acquisition and 1.88-fold acceleration compared to our standard two-fold accelerated parallel acquisition. An interchangeability study was performed, in which the ability of 6 readers to detect internal derangement of the knee was compared for the clinical and DL-accelerated images. RESULTS:The study demonstrated a high degree of interchangeability between standard and DL-accelerated images. In particular, results showed that interchanging the sequences would result in discordant clinical opinions no more than 4% of the time for any feature evaluated. Moreover, the accelerated sequence was judged by all six readers to have better quality than the clinical sequence. CONCLUSIONS:An optimized DL model allowed for acceleration of knee images which performed interchangeably with standard images for the detection of internal derangement of the knee. Importantly, readers preferred the quality of accelerated images to that of standard clinical images.
PMID: 32755163
ISSN: 1546-3141
CID: 4557132

Artificial Intelligence Explained for Nonexperts

Razavian, Narges; Knoll, Florian; Geras, Krzysztof J
Artificial intelligence (AI) has made stunning progress in the last decade, made possible largely due to the advances in training deep neural networks with large data sets. Many of these solutions, initially developed for natural images, speech, or text, are now becoming successful in medical imaging. In this article we briefly summarize in an accessible way the current state of the field of AI. Furthermore, we highlight the most promising approaches and describe the current challenges that will need to be solved to enable broad deployment of AI in clinical practice.
PMID: 31991447
ISSN: 1098-898x
CID: 4294102

Improving the Speed of MRI with Artificial Intelligence

Johnson, Patricia M; Recht, Michael P; Knoll, Florian
Magnetic resonance imaging (MRI) is a leading image modality for the assessment of musculoskeletal (MSK) injuries and disorders. A significant drawback, however, is the lengthy data acquisition. This issue has motivated the development of methods to improve the speed of MRI. The field of artificial intelligence (AI) for accelerated MRI, although in its infancy, has seen tremendous progress over the past 3 years. Promising approaches include deep learning methods for reconstructing undersampled MRI data and generating high-resolution from low-resolution data. Preliminary studies show the promise of the variational network, a state-of-the-art technique, to generalize to many different anatomical regions and achieve comparable diagnostic accuracy as conventional methods. This article discusses the state-of-the-art methods, considerations for clinical applicability, followed by future perspectives for the field.
PMID: 31991448
ISSN: 1098-898x
CID: 4294112