Akshay Chaudhari

All Publications

• Utility of deep learning super-resolution in the context of osteoarthritis MRI biomarkers. Journal of magnetic resonance imaging : JMRI Chaudhari, A. S., Stevens, K. J., Wood, J. P., Chakraborty, A. K., Gibbons, E. K., Fang, Z., Desai, A. D., Lee, J. H., Gold, G. E., Hargreaves, B. A. 2019

  Abstract

  BACKGROUND: Super-resolution is an emerging method for enhancing MRI resolution; however, its impact on image quality is still unknown.PURPOSE: To evaluate MRI super-resolution using quantitative and qualitative metrics of cartilage morphometry, osteophyte detection, and global image blurring.STUDY TYPE: Retrospective.POPULATION: In all, 176 MRI studies of subjects at varying stages of osteoarthritis.FIELD STRENGTH/SEQUENCE: Original-resolution 3D double-echo steady-state (DESS) and DESS with 3* thicker slices retrospectively enhanced using super-resolution and tricubic interpolation (TCI) at 3T.ASSESSMENT: A quantitative comparison of femoral cartilage morphometry was performed for the original-resolution DESS, the super-resolution, and the TCI scans in 17 subjects. A reader study by three musculoskeletal radiologists assessed cartilage image quality, overall image sharpness, and osteophytes incidence in all three sets of scans. A referenceless blurring metric evaluated blurring in all three image dimensions for the three sets of scans.STATISTICAL TESTS: Mann-Whitney U-tests compared Dice coefficients (DC) of segmentation accuracy for the DESS, super-resolution, and TCI images, along with the image quality readings and blurring metrics. Sensitivity, specificity, and diagnostic odds ratio (DOR) with 95% confidence intervals compared osteophyte detection for the super-resolution and TCI images, with the original-resolution as a reference.RESULTS: DC for the original-resolution (90.2±1.7%) and super-resolution (89.6±2.0%) were significantly higher (P<0.001) than TCI (86.3±5.6%). Segmentation overlap of super-resolution with the original-resolution (DC = 97.6±0.7%) was significantly higher (P<0.0001) than TCI overlap (DC = 95.0±1.1%). Cartilage image quality for sharpness and contrast levels, and the through-plane quantitative blur factor for super-resolution images, was significantly (P<0.001) better than TCI. Super-resolution osteophyte detection sensitivity of 80% (76-82%), specificity of 93% (92-94%), and DOR of 32 (22-46) was significantly higher (P<0.001) than TCI sensitivity of 73% (69-76%), specificity of 90% (89-91%), and DOR of 17 (13-22).DATA CONCLUSION: Super-resolution appears to consistently outperform naive interpolation and may improve image quality without biasing quantitative biomarkers.LEVEL OF EVIDENCE: 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019.

  View details for DOI 10.1002/jmri.26872

  View details for PubMedID 31313397

• Combined 5-minute double-echo in steady-state with separated echoes and 2-minute proton-density-weighted 2D FSE sequence for comprehensive whole-joint knee MRI assessment. Journal of magnetic resonance imaging : JMRI Chaudhari, A. S., Stevens, K. J., Sveinsson, B., Wood, J. P., Beaulieu, C. F., Oei, E. H., Rosenberg, J. K., Kogan, F., Alley, M. T., Gold, G. E., Hargreaves, B. A. 2018

  Abstract

  BACKGROUND: Clinical knee MRI protocols require upwards of 15 minutes of scan time.PURPOSE/HYPOTHESIS: To compare the imaging appearance of knee abnormalities depicted with a 5-minute 3D double-echo in steady-state (DESS) sequence with separate echo images, with that of a routine clinical knee MRI protocol. A secondary goal was to compare the imaging appearance of knee abnormalities depicted with 5-minute DESS paired with a 2-minute coronal proton-density fat-saturated (PDFS) sequence.STUDY TYPE: Prospective.SUBJECTS: Thirty-six consecutive patients (19 male) referred for a routine knee MRI.FIELD STRENGTH/SEQUENCES: DESS and PDFS at 3T.ASSESSMENT: Five musculoskeletal radiologists evaluated all images for the presence of internal knee derangement using DESS, DESS+PDFS, and the conventional imaging protocol, and their associated diagnostic confidence of the reading.STATISTICAL TESTS: Differences in positive and negative percent agreement (PPA and NPA, respectively) and 95% confidence intervals (CIs) for DESS and DESS+PDFS compared with the conventional protocol were calculated and tested using exact McNemar tests. The percentage of observations where DESS or DESS+PDFS had equivalent confidence ratings to DESS+Conv were tested with exact symmetry tests. Interreader agreement was calculated using Krippendorff's alpha.RESULTS: DESS had a PPA of 90% (88-92% CI) and NPA of 99% (99-99% CI). DESS+PDFS had increased PPA of 99% (95-99% CI) and NPA of 100% (99-100% CI) compared with DESS (both P < 0.001). DESS had equivalent diagnostic confidence to DESS+Conv in 94% of findings, whereas DESS+PDFS had equivalent diagnostic confidence in 99% of findings (both P < 0.001). All readers had moderate concordance for all three protocols (Krippendorff's alpha 47-48%).DATA CONCLUSION: Both 1) 5-minute 3D-DESS with separated echoes and 2) 5-minute 3D-DESS paired with a 2-minute coronal PDFS sequence depicted knee abnormalities similarly to a routine clinical knee MRI protocol, which may be a promising technique for abbreviated knee MRI.LEVEL OF EVIDENCE: 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018.

  View details for PubMedID 30582251

• Super-resolution musculoskeletal MRI using deep learning. Magnetic resonance in medicine Chaudhari, A. S., Fang, Z., Kogan, F., Wood, J., Stevens, K. J., Gibbons, E. K., Lee, J. H., Gold, G. E., Hargreaves, B. A. 2018

  Abstract

  PURPOSE: To develop a super-resolution technique using convolutional neural networks for generating thin-slice knee MR images from thicker input slices, and compare this method with alternative through-plane interpolation methods.METHODS: We implemented a 3D convolutional neural network entitled DeepResolve to learn residual-based transformations between high-resolution thin-slice images and lower-resolution thick-slice images at the same center locations. DeepResolve was trained using 124 double echo in steady-state (DESS) data sets with 0.7-mm slice thickness and tested on 17 patients. Ground-truth images were compared with DeepResolve, clinically used tricubic interpolation, and Fourier interpolation methods, along with state-of-the-art single-image sparse-coding super-resolution. Comparisons were performed using structural similarity, peak SNR, and RMS error image quality metrics for a multitude of thin-slice downsampling factors. Two musculoskeletal radiologists ranked the 3 data sets and reviewed the diagnostic quality of the DeepResolve, tricubic interpolation, and ground-truth images for sharpness, contrast, artifacts, SNR, and overall diagnostic quality. Mann-Whitney U tests evaluated differences among the quantitative image metrics, reader scores, and rankings. Cohen's Kappa (kappa) evaluated interreader reliability.RESULTS: DeepResolve had significantly better structural similarity, peak SNR, and RMS error than tricubic interpolation, Fourier interpolation, and sparse-coding super-resolution for all downsampling factors (p<.05, except 4*and 8*sparse-coding super-resolution downsampling factors). In the reader study, DeepResolve significantly outperformed (p<.01) tricubic interpolation in all image quality categories and overall image ranking. Both readers had substantial scoring agreement (kappa=0.73).CONCLUSION: DeepResolve was capable of resolving high-resolution thin-slice knee MRI from lower-resolution thicker slices, achieving superior quantitative and qualitative diagnostic performance to both conventionally used and state-of-the-art methods.

  View details for PubMedID 29582464

• Five-minute knee MRI for simultaneous morphometry and T2 relaxometry of cartilage and meniscus and for semiquantitative radiological assessment using double-echo in steady-state at 3T. Journal of magnetic resonance imaging : JMRI Chaudhari, A. S., Black, M. S., Eijgenraam, S., Wirth, W., Maschek, S., Sveinsson, B., Eckstein, F., Oei, E. H., Gold, G. E., Hargreaves, B. A. 2018; 47 (5): 1328–41

  Abstract

  Biomarkers for assessing osteoarthritis activity necessitate multiple MRI sequences with long acquisition times.To perform 5-minute simultaneous morphometry (thickness/volume measurements) and T2 relaxometry of both cartilage and meniscus, and semiquantitative MRI Osteoarthritis Knee Scoring (MOAKS).Prospective.Fifteen healthy volunteers for morphometry and T2 measurements, and 15 patients (five each Kellgren-Lawrence grades 0/2/3) for MOAKS assessment.A 5-minute double-echo steady-state (DESS) sequence was evaluated for generating quantitative and semiquantitative osteoarthritis biomarkers at 3T.Flip angle simulations evaluated tissue signals and sensitivity of T2 measurements. Morphometry and T2 reproducibility was compared against morphometry-optimized and relaxometry-optimized sequences. Repeatability was assessed by scanning five volunteers twice. MOAKS reproducibility was compared to MOAKS derived from a clinical knee MRI protocol by two readers.Coefficients of variation (CVs), concordance confidence intervals (CCI), and Wilcoxon signed-rank tests compared morphometry and relaxometry measurements with their reference standards. DESS MOAKS positive percent agreement (PPA), negative percentage agreement (NPA), and interreader agreement was calculated using the clinical protocol as a reference. Biomarker variations between Kellgren-Lawrence groups were evaluated using Wilcoxon rank-sum tests.Cartilage thickness (P = 0.65), cartilage T2 (P = 0.69), and meniscus T2 (P = 0.06) did not significantly differ from their reference standard (with a 20° DESS flip angle). DESS slightly overestimated meniscus volume (P < 0.001). Accuracy and repeatability CVs were <3.3%, except the meniscus T2 accuracy (7.6%). DESS MOAKS had substantial interreader agreement and high PPA/NPA values of 87%/90%. Bone marrow lesions and menisci had slightly lower PPAs. Cartilage and meniscus T2 , and MOAKS (cartilage surface area, osteophytes, cysts, and total score) was higher in Kellgren-Lawrence groups 2 and 3 than group 0 (P < 0.05).The 5-minute DESS sequence permits MOAKS assessment for a majority of tissues, along with repeatable and reproducible simultaneous cartilage and meniscus T2 relaxometry and morphometry measurements.2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018;47:1328-1341.

  View details for PubMedID 29090500

  View details for PubMedCentralID PMC5899635

• connective tissues in the knee using ultrashort echo-time double-echo steady-state (UTEDESS). Magnetic resonance in medicine Chaudhari, A. S., Sveinsson, B., Moran, C. J., McWalter, E. J., Johnson, E. M., Zhang, T., Gold, G. E., Hargreaves, B. A. 2017

  Abstract

  To develop a radial, double-echo steady-state (DESS) sequence with ultra-short echo-time (UTE) capabilities for T2 measurement of short-T2 tissues along with simultaneous rapid, signal-to-noise ratio (SNR)-efficient, and high-isotropic-resolution morphological knee imaging.THe 3D radial UTE readouts were incorporated into DESS, termed UTEDESS. Multiple-echo-time UTEDESS was used for performing T2 relaxometry for short-T2 tendons, ligaments, and menisci; and for Dixon water-fat imaging. In vivo T2 estimate repeatability and SNR efficiency for UTEDESS and Cartesian DESS were compared. The impact of coil combination methods on short-T2 measurements was evaluated by means of simulations. UTEDESS T2 measurements were compared with T2 measurements from Cartesian DESS, multi-echo spin-echo (MESE), and fast spin-echo (FSE).UTEDESS produced isotropic resolution images with high SNR efficiency in all short-T2 tissues. Simulations and experiments demonstrated that sum-of-squares coil combinations overestimated short-T2 measurements. UTEDESS measurements of meniscal T2 were comparable to DESS, MESE, and FSE measurements while the tendon and ligament measurements were less biased than those from Cartesian DESS. Average UTEDESS T2 repeatability variation was under 10% in all tissues.The T2 measurements of short-T2 tissues and high-resolution morphological imaging provided by UTEDESS makes it promising for studying the whole knee, both in routine clinical examinations and longitudinal studies. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

  View details for DOI 10.1002/mrm.26577

  View details for PubMedID 28074498

• A simple analytic method for estimating T2 in the knee from DESS. Magnetic resonance imaging SVEINSSON, B., Chaudhari, A. S., Gold, G. E., Hargreaves, B. A. 2016; 38: 63-70

  Abstract

  To introduce a simple analytical formula for estimating T2 from a single Double-Echo in Steady-State (DESS) scan.Extended Phase Graph (EPG) modeling was used to develop a straightforward linear approximation of the relationship between the two DESS signals, enabling accurate T2 estimation from one DESS scan. Simulations were performed to demonstrate cancellation of different echo pathways to validate this simple model. The resulting analytic formula was compared to previous methods for T2 estimation using DESS and fast spin-echo scans in agar phantoms and knee cartilage in three volunteers and three patients. The DESS approach allows 3D (256×256×44) T2-mapping with fat suppression in scan times of 3-4min.The simulations demonstrated that the model approximates the true signal very well. If the T1 is within 20% of the assumed T1, the T2 estimation error was shown to be less than 5% for typical scans. The inherent residual error in the model was demonstrated to be small both due to signal decay and opposing signal contributions. The estimated T2 from the linear relationship agrees well with reference scans, both for the phantoms and in vivo. The method resulted in less underestimation of T2 than previous single-scan approaches, with processing times 60 times faster than using a numerical fit.A simplified relationship between the two DESS signals allows for rapid 3D T2 quantification with DESS that is accurate, yet also simple. The simplicity of the method allows for immediate T2 estimation in cartilage during the MRI examination.

  View details for DOI 10.1016/j.mri.2016.12.018

  View details for PubMedID 28017730

  View details for PubMedCentralID PMC5360502

• Evaluation of a Flexible 12-Channel Screen-printed Pediatric MRI Coil RADIOLOGY Winkler, S., Corea, J., Lechene, B., O'Brien, K., Bonanni, J., Chauelhari, A., Alley, M., Taviani, V., Grafendorfer, T., Robb, F., Seem, G., Pauly, J., Lustig, M., Arias, A., Vasanawala, S. 2019; 291 (1): 179–84

  View details for DOI 10.1148/radiol.2019181883

  View details for Web of Science ID 000465222600036

• Simultaneous NODDI and GFA parameter map generation from subsampled q-space imaging using deep learning MAGNETIC RESONANCE IN MEDICINE Gibbons, E. K., Hodgson, K. K., Chaudhari, A. S., Richards, L. G., Majersik, J. J., Adluru, G., DiBella, E. R. 2019; 81 (4): 2399–2411

  View details for DOI 10.1002/mrm.27568

  View details for Web of Science ID 000462092100015

• Evaluation of a Flexible 12-Channel Screen-printed Pediatric MRI Coil. Radiology Winkler, S. A., Corea, J., Lechene, B., O'Brien, K., Bonanni, J. R., Chaudhari, A., Alley, M., Taviani, V., Grafendorfer, T., Robb, F., Scott, G., Pauly, J., Lustig, M., Arias, A. C., Vasanawala, S. 2019: 181883

  Abstract

  Background Screen-printed MRI coil technology may reduce the need for bulky and heavy housing of coil electronics and may provide a better fit to patient anatomy to improve coil performance. Purpose To assess the performance and caregiver and clinician acceptance of a pediatric-sized screen-printed flexible MRI coil array as compared with conventional coil technology. Materials and Methods A pediatric-sized 12-channel coil array was designed by using a screen-printing process. Element coupling and phantom signal-to-noise ratio (SNR) were assessed. Subjects were scanned by using the pediatric printed array between September and November 2017; results were compared with three age- and sex-matched historical control subjects by using a commercial 32-channel cardiac array at 3 T. Caregiver acceptance was assessed by asking nurses, technologists, anesthesiologists, and subjects or parents to rate their coil preference. Diagnostic quality of the images was evaluated by using a Likert scale (5 = high image quality, 1 = nondiagnostic). Image SNR was evaluated and compared. Results Twenty study participants were evaluated with the screen-printed coil (age range, 2 days to 12 years; 11 male and nine female subjects). Loaded pediatric phantom testing yielded similar noise covariance matrices and only slightly degraded SNR for the printed coil as compared with the commercial coil. The caregiver acceptance survey yielded a mean score of 4.1 ± 0.6 (scale: 1, preferred the commercial coil; 5, preferred the printed coil). Diagnostic quality score was 4.5 ± 0.6. Mean image SNR was 54 ± 49 (paraspinal muscle), 78 ± 51 (abdominal wall muscle), and 59 ± 35 (psoas) for the printed coil, as compared with 64 ± 55, 65 ± 48, and 57 ± 43, respectively, for the commercial coil; these SNR differences were not statistically significant (P = .26). Conclusion A flexible screen-printed pediatric MRI receive coil yields adequate signal-to-noise ratio in phantoms and pediatric study participants, with similar image quality but higher preference by subjects and their caregivers when compared with a conventional MRI coil. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Lamb in this issue.

  View details for PubMedID 30806599

• Simultaneous NODDI and GFA parameter map generation from subsampled q-space imaging using deep learning. Magnetic resonance in medicine Gibbons, E. K., Hodgson, K. K., Chaudhari, A. S., Richards, L. G., Majersik, J. J., Adluru, G., DiBella, E. V. 2018

  Abstract

  PURPOSE: To develop a robust multidimensional deep-learning based method to simultaneously generate accurate neurite orientation dispersion and density imaging (NODDI) and generalized fractional anisotropy (GFA) parameter maps from undersampled q-space datasets for use in stroke imaging.METHODS: Traditional diffusion spectrum imaging (DSI) capable of producing accurate NODDI and GFA parameter maps requires hundreds of q-space samples which renders the scan time clinically untenable. A convolutional neural network (CNN) was trained to generated NODDI and GFA parameter maps simultaneously from 10* undersampled q-space data. A total of 48 DSI scans from 15 stroke patients and 14 normal subjects were acquired for training, validating, and testing this method. The proposed network was compared to previously proposed voxel-wise machine learning based approaches for q-space imaging. Network-generated images were used to predict stroke functional outcome measures.RESULTS: The proposed network achieves significant performance advantages compared to previously proposed machine learning approaches, showing significant improvements across image quality metrics. Generating these parameter maps using CNNs also comes with the computational benefits of only needing to generate and train a single network instead of multiple networks for each parameter type. Post-stroke outcome prediction metrics do not appreciably change when using images generated from this proposed technique. Over three test participants, the predicted stroke functional outcome scores were within 1-6% of the clinical evaluations.CONCLUSIONS: Estimates of NODDI and GFA parameters estimated simultaneously with a deep learning network from highly undersampled q-space data were improved compared to other state-of-the-art methods providing a 10-fold reduction scan time compared to conventional methods.

  View details for PubMedID 30426558

• 3D Ultrashort TE MRI for Evaluation of Cartilaginous Endplate of Cervical Disk In Vivo: Feasibility and Correlation With Disk Degeneration in T2-Weighted Spin-Echo Sequence AMERICAN JOURNAL OF ROENTGENOLOGY Kim, Y., Cha, J., Shin, Y., Chaudhari, A. S., Suh, Y., Yoon, S., Gold, G. E. 2018; 210 (5): 1131–40

  Abstract

  The purpose of this study was to evaluate the feasibility of 3D ultrashort TE (UTE) MRI in depicting the cartilaginous endplate (CEP) and its abnormalities and to investigate the association between CEP abnormalities and disk degeneration on T2-weighted spin-echo (SE) MR images in cervical disks in vivo.Eight healthy volunteers and 70 patients were examined using 3-T MRI with the 3D UTE cones trajectory technique (TR/TE, 16.1/0.032, 6.6). In the volunteer study, quantitative and qualitative assessments of CEP depiction were conducted for the 3D UTE and T2-weighted SE imaging. In the patient study, CEP abnormalities were analyzed. Intersequence agreement between the images obtained with the first-echo 3D UTE sequence and the images created by subtracting the second-echo from the first-echo 3D UTE sequence (subtracted 3D UTE) and the intraobserver and interobserver agreements for 3D UTE overall were also tested. The CEP abnormalities on the 3D UTE images correlated with the Miyazaki grading of the T2-weighted SE images.In the volunteer study, the CEP was well visualized on 3D UTE images but not on T2-weighted SE images (p < 0.001). In the patient study, for evaluation of CEP abnormalities, intersequence agreements were substantial to almost perfect, intraobserver agreements were substantial to almost perfect, and interobserver agreements were moderate to substantial (p < 0.001). All of the CEP abnormalities correlated with the Miyazaki grade with statistical significance (p < 0.001).Three-dimensional UTE MRI feasibly depicts the CEP and CEP abnormalities, which may be associated with the severity of disk degeneration on T2-weighted SE MRI.

  View details for PubMedID 29629793

• Simultaneous bilateral-knee MR imaging. Magnetic resonance in medicine Kogan, F., Levine, E., Chaudhari, A. S., Monu, U. D., Epperson, K., Oei, E. H., Gold, G. E., Hargreaves, B. A. 2018; 80 (2): 529–37

  Abstract

  To demonstrate and evaluate the scan time and quantitative accuracy of simultaneous bilateral-knee imaging compared with single-knee acquisitions.Hardware modifications and safety testing was performed to enable MR imaging with two 16-channel flexible coil arrays. Noise covariance and sensitivity-encoding g-factor maps for the dual-coil-array configuration were computed to evaluate coil cross-talk and noise amplification. Ten healthy volunteers were imaged on a 3T MRI scanner with both dual-coil-array bilateral-knee and single-coil-array single-knee configurations. Two experienced musculoskeletal radiologists compared the relative image quality between blinded image pairs acquired with each configuration. Differences in T2 relaxation time measurements between dual-coil-array and single-coil-array acquisitions were compared with the standard repeatability of single-coil-array measurements using a Bland-Altman analysis.The mean g-factors for the dual-coil-array configuration were low for accelerations up to 6 in the right-left direction, and minimal cross-talk was observed between the two coil arrays. Image quality ratings of various joint tissues showed no difference in 89% (95% confidence interval: 85-93%) of rated image pairs, with only small differences ("slightly better" or "slightly worse") in image quality observed. The T2 relaxation time measurements between the dual-coil-array configuration and the single-coil configuration showed similar limits of agreement and concordance correlation coefficients (limits of agreement: -0.93 to 1.99 ms; CCC: 0.97 (95% confidence interval: 0.96-0.98)), to the repeatability of single-coil-array measurements (limits of agreement: -2.07 to 1.96 ms; CCC: 0.97 (95% confidence interval: 0.95-0.98)).A bilateral coil-array setup can image both knees simultaneously in similar scan times as conventional unilateral knee scans, with comparable image quality and quantitative accuracy. This has the potential to improve the value of MRI knee evaluations. Magn Reson Med 80:529-537, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

  View details for PubMedID 29250856

  View details for PubMedCentralID PMC5910219

• A simple analytic method for estimating T2 in the knee from DESS MAGNETIC RESONANCE IMAGING Sveinsson, B., Chaudhari, A. S., Gold, G. E., Hargreaves, B. A. 2017; 38: 63-70

  Abstract

  To introduce a simple analytical formula for estimating T2 from a single Double-Echo in Steady-State (DESS) scan.Extended Phase Graph (EPG) modeling was used to develop a straightforward linear approximation of the relationship between the two DESS signals, enabling accurate T2 estimation from one DESS scan. Simulations were performed to demonstrate cancellation of different echo pathways to validate this simple model. The resulting analytic formula was compared to previous methods for T2 estimation using DESS and fast spin-echo scans in agar phantoms and knee cartilage in three volunteers and three patients. The DESS approach allows 3D (256×256×44) T2-mapping with fat suppression in scan times of 3-4min.The simulations demonstrated that the model approximates the true signal very well. If the T1 is within 20% of the assumed T1, the T2 estimation error was shown to be less than 5% for typical scans. The inherent residual error in the model was demonstrated to be small both due to signal decay and opposing signal contributions. The estimated T2 from the linear relationship agrees well with reference scans, both for the phantoms and in vivo. The method resulted in less underestimation of T2 than previous single-scan approaches, with processing times 60 times faster than using a numerical fit.A simplified relationship between the two DESS signals allows for rapid 3D T2 quantification with DESS that is accurate, yet also simple. The simplicity of the method allows for immediate T2 estimation in cartilage during the MRI examination.

  View details for DOI 10.1016/j.mri.2016.12.018

  View details for Web of Science ID 000398008700010

  View details for PubMedCentralID PMC5360502