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fastMRI+, Clinical pathology annotations for knee and brain fully sampled magnetic resonance imaging data

Zhao, Ruiyang; Yaman, Burhaneddin; Zhang, Yuxin; Stewart, Russell; Dixon, Austin; Knoll, Florian; Huang, Zhengnan; Lui, Yvonne W; Hansen, Michael S; Lungren, Matthew P
Improving speed and image quality of Magnetic Resonance Imaging (MRI) using deep learning reconstruction is an active area of research. The fastMRI dataset contains large volumes of raw MRI data, which has enabled significant advances in this field. While the impact of the fastMRI dataset is unquestioned, the dataset currently lacks clinical expert pathology annotations, critical to addressing clinically relevant reconstruction frameworks and exploring important questions regarding rendering of specific pathology using such novel approaches. This work introduces fastMRI+, which consists of 16154 subspecialist expert bounding box annotations and 13 study-level labels for 22 different pathology categories on the fastMRI knee dataset, and 7570 subspecialist expert bounding box annotations and 643 study-level labels for 30 different pathology categories for the fastMRI brain dataset. The fastMRI+ dataset is open access and aims to support further research and advancement of medical imaging in MRI reconstruction and beyond.
PMCID:8983757
PMID: 35383186
ISSN: 2052-4463
CID: 5201602

A No-Math Primer on the Principles of Machine Learning for Radiologists

Lee, Matthew D; Elsayed, Mohammed; Chopra, Sumit; Lui, Yvonne W
Machine learning is becoming increasingly important in both research and clinical applications in radiology due to recent technological developments, particularly in deep learning. As these technologies are translated toward clinical practice, there is a need for radiologists and radiology trainees to understand the basic principles behind them. This primer provides an accessible introduction to the vocabulary and concepts that are central to machine learning and relevant to the radiologist.
PMID: 35339253
ISSN: 1558-5034
CID: 5190662

Radial spoiled gradient T1 weighted imaging of the internal auditory canal: Is Scarpa's ganglion now an expected finding and source of fundal enhancement?

Munawar, Kamran; Raz, Eytan; Dehkharghani, Seena; Fatterpekar, Girish M; Block, Tobias K; Lui, Yvonne W
StarVIBE is a 3D gradient-echo sequence with a radial, stack-of-stars acquisition having spatial resolution and tissue contrast. With newer sequences, it is important to be familiar with sequence tissue contrasts and appearance of anatomical variants. We evaluated 450 patients utilizing this sequence; 35 patients demonstrated fluffy "cotton wool" enhancement at the internal auditory canal fundus without clear pathology. We favor this represents anatomic neurovascular enhancement that StarVIBE is sensitive to and is a touch-me-not finding.
PMID: 35015577
ISSN: 2385-1996
CID: 5118602

Development and Practical Implementation of a Deep Learning-Based Pipeline for Automated Pre- and Postoperative Glioma Segmentation

Lotan, E; Zhang, B; Dogra, S; Wang, W D; Carbone, D; Fatterpekar, G; Oermann, E K; Lui, Y W
BACKGROUND AND PURPOSE/OBJECTIVE:Quantitative volumetric segmentation of gliomas has important implications for diagnosis, treatment, and prognosis. We present a deep-learning model that accommodates automated preoperative and postoperative glioma segmentation with a pipeline for clinical implementation. Developed and engineered in concert, the work seeks to accelerate clinical realization of such tools. MATERIALS AND METHODS/METHODS:A deep learning model, autoencoder regularization-cascaded anisotropic, was developed, trained, and tested fusing key elements of autoencoder regularization with a cascaded anisotropic convolutional neural network. We constructed a dataset consisting of 437 cases with 40 cases reserved as a held-out test and the remainder split 80:20 for training and validation. We performed data augmentation and hyperparameter optimization and used a mean Dice score to evaluate against baseline models. To facilitate clinical adoption, we developed the model with an end-to-end pipeline including routing, preprocessing, and end-user interaction. RESULTS:The autoencoder regularization-cascaded anisotropic model achieved median and mean Dice scores of 0.88/0.83 (SD, 0.09), 0.89/0.84 (SD, 0.08), and 0.81/0.72 (SD, 0.1) for whole-tumor, tumor core/resection cavity, and enhancing tumor subregions, respectively, including both preoperative and postoperative follow-up cases. The overall total processing time per case was ∼10 minutes, including data routing (∼1 minute), preprocessing (∼6 minute), segmentation (∼1-2 minute), and postprocessing (∼1 minute). Implementation challenges were discussed. CONCLUSIONS:We show the feasibility and advantages of building a coordinated model with a clinical pipeline for the rapid and accurate deep learning segmentation of both preoperative and postoperative gliomas. The ability of the model to accommodate cases of postoperative glioma is clinically important for follow-up. An end-to-end approach, such as used here, may lead us toward successful clinical translation of tools for quantitative volume measures for glioma.
PMID: 34857514
ISSN: 1936-959x
CID: 5069232

Multi-shell diffusion MR imaging and brain microstructure after mild traumatic brain injury: A focus on working memory

Chapter by: Chung, Sohae; Fieremans, Els; Rath, Joseph; Lui, Yvonne
in: Neuroscience of Traumatic Brain Injury by Rejendram, Rajkumar; Preedy, Victor; Martin, Colin
[S.l.] : Elsevier, 2022
pp. -
ISBN: 9780323991971
CID: 5110812

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

Simultaneous Multislice for Accelerating Diffusion MRI in Clinical Neuroradiology Protocols

Hoch, M J; Bruno, M; Pacione, D; Lui, Y W; Fieremans, E; Shepherd, T M
BACKGROUND AND PURPOSE/OBJECTIVE:Diffusion MR imaging sequences essential for clinical neuroradiology imaging protocols may be accelerated with simultaneous multislice acquisitions. We tested whether simultaneous multislice-accelerated diffusion data were clinically equivalent to standard acquisitions. MATERIALS AND METHODS/METHODS:; 60 directions). The corticospinal tract and arcuate fasciculus ipsilateral to the lesion were generated using the same ROIs and then blindly assessed by a neurosurgeon for anatomic fidelity, perceived quality, and impact on surgical management. Tract volumes were compared for spatial overlap. RESULTS:Two-slice simultaneous multislice diffusion reduced acquisition times from 141 to 45 seconds for routine diffusion and from 7.5 to 5.9 minutes for diffusion tractography using 3T MR imaging. The simultaneous multislice-accelerated diffusion sequence was rated equivalent for diagnostic utility despite reductions to perceived image quality. Simultaneous multislice-accelerated diffusion tractography was rated clinically equivalent. Dice similarity coefficients between routine and simultaneous multislice-generated corticospinal tract and arcuate fasciculus tract volumes were 0.78 (SD, 0.03) and 0.71 (SD, 0.05), respectively. CONCLUSIONS:-space-resolution diffusion acquisitions required for translating advanced diffusion models into clinical practice.
PMID: 33985946
ISSN: 1936-959x
CID: 4868222

An artificial intelligence system for predicting the deterioration of COVID-19 patients in the emergency department

Shamout, Farah E; Shen, Yiqiu; Wu, Nan; Kaku, Aakash; Park, Jungkyu; Makino, Taro; Jastrzębski, Stanisław; Witowski, Jan; Wang, Duo; Zhang, Ben; Dogra, Siddhant; Cao, Meng; Razavian, Narges; Kudlowitz, David; Azour, Lea; Moore, William; Lui, Yvonne W; Aphinyanaphongs, Yindalon; Fernandez-Granda, Carlos; Geras, Krzysztof J
During the coronavirus disease 2019 (COVID-19) pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3661 patients, achieves an area under the receiver operating characteristic curve (AUC) of 0.786 (95% CI: 0.745-0.830) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at New York University Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.
PMID: 33980980
ISSN: 2398-6352
CID: 4867572

Impact of Kidney Function on CNS Gadolinium Deposition in Patients Receiving Repeated Doses of Gadobutrol

Dogra, S; Borja, M J; Lui, Y W
BACKGROUND AND PURPOSE/OBJECTIVE:Studies associate repeat gadolinium-based contrast agent administration with T1 shortening in the dentate nucleus and globus pallidus, indicating CNS gadolinium deposition, most strongly with linear agents but also reportedly with macrocyclics. Renal impairment effects on long-term CNS gadolinium deposition remain underexplored. We investigated the relationship between signal intensity changes and renal function in patients who received ≥10 administrations of the macrocyclic agent gadobutrol. MATERIALS AND METHODS/METHODS:Patients who underwent ≥10 brain MR imaging examinations with administration of intravenous gadobutrol between February 1, 2014, and January 1, 2018, were included in this retrospective study. Dentate nucleus-to-pons and globus pallidus-to-thalamus signal intensity ratios were calculated, and correlations were calculated between the estimated glomerular filtration rate (minimum and mean) and the percentage change in signal intensity ratios from the first to last scan. Partial correlations were calculated to control for potential confounders. RESULTS:= .09). CONCLUSIONS:In patients receiving an average of 12 intravenous gadobutrol administrations, no correlation was found between renal function and signal intensity ratio changes, even in those with mild or moderate renal impairment.
PMID: 33632738
ISSN: 1936-959x
CID: 4802372

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