Ali Bin Syed

All Publications

• Artifact- and content-specific quality assessment for MRI with image rulers. Medical image analysis Lei, K., Syed, A. B., Zhu, X., Pauly, J. M., Vasanawala, S. S. 1800; 77: 102344

  Abstract

  In clinical practice MR images are often first seen by radiologists long after the scan. If image quality is inadequate either patients have to return for an additional scan, or a suboptimal interpretation is rendered. An automatic image quality assessment (IQA) would enable real-time remediation. Existing IQA works for MRI give only a general quality score, agnostic to the cause of and solution to low-quality scans. Furthermore, radiologists' image quality requirements vary with the scan type and diagnostic task. Therefore, the same score may have different implications for different scans. We propose a framework with multi-task CNN model trained with calibrated labels and inferenced with image rulers. Labels calibrated by human inputs follow a well-defined and efficient labeling task. Image rulers address varying quality standards and provide a concrete way of interpreting raw scores from the CNN. The model supports assessments of two of the most common artifacts in MRI: noise and motion. It achieves accuracies of around 90%, 6% better than the best previous method examined, and 3% better than human experts on noise assessment. Our experiments show that label calibration, image rulers, and multi-task training improve the model's performance and generalizability.

  View details for DOI 10.1016/j.media.2021.102344

  View details for PubMedID 35091278

• Free-breathing R 2 ∗ mapping of hepatic iron overload in children using 3D multi-echo UTE cones MRI. Magnetic resonance in medicine Kee, Y. n., Sandino, C. M., Syed, A. B., Cheng, J. Y., Shimakawa, A. n., Colgan, T. J., Hernando, D. n., Vasanawala, S. S. 2021

  Abstract

  To enable motion-robust, ungated, free-breathing R 2 ∗ mapping of hepatic iron overload in children with 3D multi-echo UTE cones MRI.A golden-ratio re-ordered 3D multi-echo UTE cones acquisition was developed with chemical-shift encoding (CSE). Multi-echo complex-valued source images were reconstructed via gridding and coil combination, followed by confounder-corrected R 2 ∗ (=1/ T 2 ∗ ) mapping. A phantom containing 15 different concentrations of gadolinium solution (0-300 mM) was imaged at 3T. 3D multi-echo UTE cones with an initial TE of 0.036 ms and Cartesian CSE-MRI (IDEAL-IQ) sequences were performed. With institutional review board approval, 85 subjects (81 pediatric patients with iron overload + 4 healthy volunteers) were imaged at 3T using 3D multi-echo UTE cones with free breathing (FB cones), IDEAL-IQ with breath holding (BH Cartesian), and free breathing (FB Cartesian). Overall image quality of R 2 ∗ maps was scored by 2 blinded experts and compared by a Wilcoxon rank-sum test. For each pediatric subject, the paired R 2 ∗ maps were assessed to determine if a corresponding artifact-free 15 mm region-of-interest (ROI) could be identified at a mid-liver level on both images. Agreement between resulting R 2 ∗ quantification from FB cones and BH/FB Cartesian was assessed with Bland-Altman and linear correlation analyses.ROI-based regression analysis showed a linear relationship between gadolinium concentration and R 2 ∗ in IDEAL-IQ (y = 8.83x - 52.10, R2 = 0.995) as well as in cones (y = 9.19x - 64.16, R2 = 0.992). ROI-based Bland-Altman analysis showed that the mean difference (MD) was 0.15% and the SD was 5.78%. However, IDEAL-IQ R 2 ∗ measurements beyond 200 mM substantially deviated from a linear relationship for IDEAL-IQ (y = 5.85x + 127.61, R2 = 0.827), as opposed to cones (y = 10.87x - 166.96, R2 = 0.984). In vivo, FB cones R 2 ∗ had similar image quality with BH and FB Cartesian in 15 and 42 cases, respectively. FB cones R 2 ∗ had better image quality scores than BH and FB Cartesian in 3 and 21 cases, respectively, where BH/FB Cartesian exhibited severe ghosting artifacts. ROI-based Bland-Altman analyses were 2.23% (MD) and 6.59% (SD) between FB cones and BH Cartesian and were 0.21% (MD) and 7.02% (SD) between FB cones and FB Cartesian, suggesting a good agreement between FB cones and BH (FB) Cartesian R 2 ∗ . Strong linear relationships were observed between BH Cartesian and FB cones (y = 1.00x + 1.07, R2 = 0.996) and FB Cartesian and FB cones (y = 0.98x + 1.68, R2 = 0.999).Golden-ratio re-ordered 3D multi-echo UTE Cones MRI enabled motion-robust, ungated, and free-breathing R 2 ∗ mapping of hepatic iron overload, with comparable R 2 ∗ measurements and image quality to BH Cartesian, and better image quality than FB Cartesian.

  View details for DOI 10.1002/mrm.28610

  View details for PubMedID 33432613

• Rosette Trajectories Enable Ungated, Motion-Robust, Simultaneous Cardiac and Liver T2 * Iron Assessment. Journal of magnetic resonance imaging : JMRI Bush, A. M., Sandino, C. M., Ramachandran, S., Ong, F., Dwork, N., Zucker, E. J., Syed, A. B., Pauly, J. M., Alley, M. T., Vasanawala, S. S. 2020: e27196

  Abstract

  BACKGROUND: Quantitative T2 * MRI is the standard of care for the assessment of iron overload. However, patient motion corrupts T2 * estimates.PURPOSE: To develop and evaluate a motion-robust, simultaneous cardiac and liver T2 * imaging approach using non-Cartesian, rosette sampling and a model-based reconstruction as compared to clinical-standard Cartesian MRI.STUDY TYPE: Prospective.PHANTOM/POPULATION: Six ferumoxytol-containing phantoms (26-288mug/mL). Eight healthy subjects and 18 patients referred for clinically indicated iron overload assessment.FIELD STRENGTH/SEQUENCE: 1.5T, 2D Cartesian and rosette gradient echo (GRE) ASSESSMENT: GRE T2 * values were validated in ferumoxytol phantoms. In healthy subjects, test-retest and spatial coefficient of variation (CoV) analysis was performed during three breathing conditions. Cartesian and rosette T2 * were compared using correlation and Bland-Altman analysis. Images were rated by three experienced radiologists on a 5-point scale.STATISTICAL TESTS: Linear regression, analysis of variance (ANOVA), and paired Student's t-testing were used to compare reproducibility and variability metrics in Cartesian and rosette scans. The Wilcoxon rank test was used to assess reader score comparisons and reader reliability was measured using intraclass correlation analysis.RESULTS: Rosette R2* (1/T2 *) was linearly correlated with ferumoxytol concentration (r2 = 1.00) and not significantly different than Cartesian values (P = 0.16). During breath-holding, ungated rosette liver and heart T2 * had lower spatial CoV (liver: 18.4±9.3% Cartesian, 8.8%±3.4% rosette, P = 0.02, heart: 37.7%±14.3% Cartesian, 13.4%±1.7% rosette, P = 0.001) and higher-quality scores (liver: 3.3 [3.0-3.6] Cartesian, 4.7 [4.1-4.9] rosette, P = 0.005, heart: 3.0 [2.3-3] Cartesian, 4.5 [3.8-5.0] rosette, P = 0.005) compared to Cartesian values. During free-breathing and failed breath-holding, Cartesian images had very poor to average image quality with significant artifacts, whereas rosette remained very good, with minimal artifacts (P = 0.001).DATA CONCLUSION: Rosette k-sampling with a model-based reconstruction offers a clinically useful motion-robust T2 * mapping approach for iron quantification.

  View details for DOI 10.1002/jmri.27196

  View details for PubMedID 32452088

• DIAGNOSTIC IMAGE QUALITY ASSESSMENT AND CLASSIFICATION IN MEDICAL IMAGING: OPPORTUNITIES AND CHALLENGES. Proceedings. IEEE International Symposium on Biomedical Imaging Ma, J. J., Nakarmi, U., Kin, C. Y., Sandino, C. M., Cheng, J. Y., Syed, A. B., Wei, P., Pauly, J. M., Vasanawala, S. S. 2020; 2020: 337-340

  Abstract

  Magnetic Resonance Imaging (MRI) suffers from several artifacts, the most common of which are motion artifacts. These artifacts often yield images that are of non-diagnostic quality. To detect such artifacts, images are prospectively evaluated by experts for their diagnostic quality, which necessitates patient-revisits and rescans whenever non-diagnostic quality scans are encountered. This motivates the need to develop an automated framework capable of accessing medical image quality and detecting diagnostic and non-diagnostic images. In this paper, we explore several convolutional neural network-based frameworks for medical image quality assessment and investigate several challenges therein.

  View details for DOI 10.1109/isbi45749.2020.9098735

  View details for PubMedID 33274013

  View details for PubMedCentralID PMC7710391

• DIAGNOSTIC IMAGE QUALITY ASSESSMENT AND CLASSIFICATION IN MEDICAL IMAGING: OPPORTUNITIES AND CHALLENGES Ma, J. J., Nakarmi, U., Kin, C., Sandino, C. M., Cheng, J. Y., Syed, A. B., Wei, P., Pauly, J. M., Vasanawala, S. S., IEEE IEEE. 2020: 337–40

  View details for Web of Science ID 000578080300058

• Near-Silent and Distortion-Free Diffusion MRI in Pediatric Musculoskeletal Disorders: Comparison With Echo Planar Imaging Diffusion. Journal of magnetic resonance imaging : JMRI Sandberg, J. K., Young, V. A., Syed, A. B., Yuan, J. n., Hu, Y. n., Sandino, C. n., Menini, A. n., Hargreaves, B. n., Vasanawala, S. n. 2020

  Abstract

  Diffusion-weighted imaging (DWI) is common for evaluating pediatric musculoskeletal lesions, but suffers from geometric distortion and intense acoustic noise.To investigate the performance of a near-silent and distortion-free DWI sequence (DW-SD) relative to standard echo-planar DWI (DW-EPI) in pediatric extremity MRI.Prospective validation study.Thirty-nine children referred for extremity MRI.DW-EPI and DW-SD, based on a rotating ultrafast sequence modified with sinusoidal diffusion preparation gradients, at 3T.DW-SD image quality (Sanat ) was assessed from 0 (nondiagnostic) to 5 (outstanding) and comparative image quality (Scomp ) (from -2 = DW-EPI more delineated to +2 = DW-SD more delineated, 0 = same). ADC measured by DW-SD and DW-EPI were compared in bone marrow, muscle, and lesions.Wilcoxon rank-sum test and confidence interval of proportions (CIOP) were calculated for Scomp , Student's t-test, coefficient of variation (COV), and Bland-Altman analysis for ADC values, and intraclass correlation coefficient (ICC) for interreader agreement.DW-SD and DW-EPI ADC values for bone marrow, muscle, and lesions were not significantly different (P = 0.3, P = 0.2, and P = 0.27, respectively) and had an overall ADC COV of 14.8% (95% confidence interval: 12.3%, 16.9%) and no significant proportional bias on Bland-Altman analysis. Sanat CIOP was rated diagnostic or better (score of 3, 4, or 5) in 72-98% of cases for bone marrow, muscle, and soft tissues. DW-SD was equivalent to or preferred over DW-EPI in muscles and soft tissues, with CIOP 86-93% and 93%, respectively. Lesions were equally visualized on DW-SD and DW-EPI in 40-51%, with DW-SD preferred in 44-56% of cases. DW-SD was rated significantly better than DW-EPI across all comparative variables that included bone marrow, muscle, soft tissue, cartilage, and lesions (P < 0.05). Readers had moderate to near-perfect (ICC range = 0.45-0.85).DW-SD of the extremities provided similar ADC values and improved image quality compared with conventional DW-EPI.2 TECHNICAL EFFICACY STAGE: 2.

  View details for DOI 10.1002/jmri.27330

  View details for PubMedID 32815203

• AI Accelerated Human-in-the-loop Structuring of Radiology Reports. AMIA ... Annual Symposium proceedings. AMIA Symposium Wu, J. T., Syed, A., Ahmad, H., Pillai, A., Gur, Y., Jadhav, A., Gruhl, D., Kato, L., Moradi, M., Syeda-Mahmood, T. 2020; 2020: 1305–14

  Abstract

  Rule-based Natural Language Processing (NLP) pipelines depend on robust domain knowledge. Given the long tail of important terminology in radiology reports, it is not uncommon for standard approaches to miss items critical for understanding the image. AI techniques can accelerate the concept expansion and phrasal grouping tasks to efficiently create a domain specific lexicon ontology for structuring reports. Using Chest X-ray (CXR) reports as an example, we demonstrate that with robust vocabulary, even a simple NLP pipeline can extract 83 directly mentioned abnormalities (Ave. recall=93.83%, precision=94.87%) and 47 abnormality/normality descriptions of key anatomies. The richer vocabulary enables identification of additional label mentions in 10 out of 13 labels (compared to baseline methods). Furthermore, it captures expert insight into critical differences between observed and inferred descriptions, and image quality issues in reports. Finally, we show how the CXR ontology can be used to anatomically structure labeled output.

  View details for PubMedID 33936507