Publications

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Publications

  • From microscope to head-mounted display: integrating hand tracking into microsurgical augmented reality. International journal of computer assisted radiology and surgery El Chemaly, T., Athayde Neves, C., Fu, F., Hargreaves, B., Blevins, N. H. 2024

    Abstract

    The operating microscope plays a central role in middle and inner ear procedures that involve working within tightly confined spaces under limited exposure. Augmented reality (AR) may improve surgical guidance by combining preoperative computed tomography (CT) imaging that can provide precise anatomical information, with intraoperative microscope video feed. With current technology, the operator must manually interact with the AR interface using a computer. The latter poses a disruption in the surgical flow and is suboptimal for maintaining the sterility of the operating environment. The purpose of this study was to implement and evaluate free-hand interaction concepts leveraging hand tracking and gesture recognition as an attempt to reduce the disruption during surgery and improve human-computer interaction.An electromagnetically tracked surgical microscope was calibrated using a custom 3D printed calibration board. This allowed the augmentation of the microscope feed with segmented preoperative CT-derived virtual models. Ultraleap's Leap Motion Controller 2 was coupled to the microscope and used to implement hand-tracking capabilities. End-user feedback was gathered from a surgeon during development. Finally, users were asked to complete tasks that involved interacting with the virtual models, aligning them to physical targets, and adjusting the AR visualization.Following observations and user feedback, we upgraded the functionalities of the hand interaction system. User feedback showed the users' preference for the new interaction concepts that provided minimal disruption of the surgical workflow and more intuitive interaction with the virtual content.We integrated hand interaction concepts, typically used with head-mounted displays (HMDs), into a surgical stereo microscope system intended for AR in otologic microsurgery. The concepts presented in this study demonstrated a more favorable approach to human-computer interaction in a surgical context. They hold potential for a more efficient execution of surgical tasks under microscopic AR guidance.

    View details for DOI 10.1007/s11548-024-03224-w

    View details for PubMedID 39162975

    View details for PubMedCentralID 4710572

  • Distortion-free water-fat separated diffusion-weighted imaging using spatiotemporal joint reconstruction. Magnetic resonance in medicine Zhou, X., Daniel, B. L., Hargreaves, B. A., Lee, P. K. 2024

    Abstract

    PURPOSE: Diffusion-weighted imaging (DWI) suffers from geometric distortion and chemical shift artifacts due to the commonly used Echo Planar Imaging (EPI) trajectory. Even with fat suppression in DWI, severe B0 and B1 variations can result in residual fat, which becomes both a source of image artifacts and a confounding factor in diffusion-weighted contrast in distinguishing benign and malignant tissues. This work presents a method for acquiring distortion-free diffusion-weighted images using spatiotemporal acquisition and joint reconstruction. Water-fat separation is performed by chemical-shift encoding.METHODS: Spatiotemporal acquisition is employed to obtain distortion-free images at a series of echo times. Chemical-shift encoding is used for water-fat separation. Reconstruction and separation are performed jointly in the spat-spectral domain. To address the shot-to-shot motion-induced phase in DWI, an Fast Spin Echo (FSE)-based phase navigator is incorporated into the sequence to obtain distortion-free phase information. The proposed method was validated in phantoms and in vivo for the brain, head and neck, and breast.RESULTS: The proposed method enables the acquisition of distortion-free diffusion-weighted images in the presence of B0 field inhomogenieties commonly observed in the body. Water and fat components are separated with no obvious spectral leakage artifacts. The estimated Apparent Diffusion Coefficient (ADC) is comparable to that of multishot DW-EPI.CONCLUSION: Distortion-free, water-fat separated diffusion-weighted images in body can be obtained through the utilization of spatiotemporal acquisition and joint reconstruction methods.

    View details for DOI 10.1002/mrm.30221

    View details for PubMedID 39051729

  • Comprehensive assessment of nonuniform image quality: Application to imaging near metal. Magnetic resonance in medicine Toews, A. R., Lee, P. K., Nayak, K. S., Hargreaves, B. A. 2024

    Abstract

    Comprehensive assessment of image quality requires accounting for spatial variations in (i) intensity artifact, (ii) geometric distortion, (iii) signal-to-noise ratio (SNR), and (iv) spatial resolution, among other factors. This work presents an ensemble of methods to meet this need, from phantom design to image analysis, and applies it to the scenario of imaging near metal.A modular phantom design employing a gyroid lattice is developed to enable the co-registered volumetric quantitation of image quality near a metallic hip implant. A method for measuring spatial resolution by means of local point spread function (PSF) estimation is presented and the relative fitness of gyroid and cubic lattices is examined. Intensity artifact, geometric distortion, and SNR maps are also computed. Results are demonstrated with 2D-FSE and MAVRIC-SL scan protocols on a 3T MRI scanner.The spatial resolution method demonstrates a worst-case error of 0.17 pixels for measuring in-plane blurring up to 3 pixels (full width at half maximum). The gyroid outperforms a cubic lattice design for the local PSF estimation task. The phantom supports four configurations toggling the presence/absence of both metal and structure with good spatial correspondence for co-registered analysis of the four quality factors. The marginal scan time to evaluate one scan protocol amounts to five repetitions. The phantom design can be fabricated in 2 days at negligible material cost.The phantom and associated analysis methods can elucidate complex image quality trade-offs involving intensity artifact, geometric distortion, SNR, and spatial resolution. The ensemble of methods is suitable for benchmarking imaging performance near metal.

    View details for DOI 10.1002/mrm.30222

    View details for PubMedID 38997797

  • ShapeMed-Knee: A Dataset and Neural Shape Model Benchmark for Modeling 3D Femurs. medRxiv : the preprint server for health sciences Gatti, A. A., Blankemeier, L., Van Veen, D., Hargreaves, B., Delp, S. L., Gold, G. E., Kogan, F., Chaudhari, A. S. 2024

    Abstract

    Analyzing anatomic shapes of tissues and organs is pivotal for accurate disease diagnostics and clinical decision-making. One prominent disease that depends on anatomic shape analysis is osteoarthritis, which affects 30 million Americans. To advance osteoarthritis diagnostics and prognostics, we introduce ShapeMed-Knee, a 3D shape dataset with 9,376 high-resolution, medical-imaging-based 3D shapes of both femur bone and cartilage. Besides data, ShapeMed-Knee includes two benchmarks for assessing reconstruction accuracy and five clinical prediction tasks that assess the utility of learned shape representations. Leveraging ShapeMed-Knee, we develop and evaluate a novel hybrid explicit-implicit neural shape model which achieves up to 40% better reconstruction accuracy than a statistical shape model and implicit neural shape model. Our hybrid models achieve state-of-the-art performance for preserving cartilage biomarkers; they're also the first models to successfully predict localized structural features of osteoarthritis, outperforming shape models and convolutional neural networks applied to raw magnetic resonance images and segmentations. The ShapeMed-Knee dataset provides medical evaluations to reconstruct multiple anatomic surfaces and embed meaningful disease-specific information. ShapeMed-Knee reduces barriers to applying 3D modeling in medicine, and our benchmarks highlight that advancements in 3D modeling can enhance the diagnosis and risk stratification for complex diseases. The dataset, code, and benchmarks will be made freely accessible.

    View details for DOI 10.1101/2024.05.06.24306965

    View details for PubMedID 38766040

  • Reproducibility of Quantitative Double-Echo Steady-State T2 Mapping of Knee Cartilage. Journal of magnetic resonance imaging : JMRI Williams, A. A., Asay, J. L., Asare, D., Desai, A. D., Gold, G. E., Hargreaves, B. A., Chaudhari, A. S., Chu, C. R. 2024

    Abstract

    Cartilage T2 can detect joints at risk of developing osteoarthritis. The quantitative double-echo steady state (qDESS) sequence is attractive for knee cartilage T2 mapping because of its acquisition time of under 5 minutes. Understanding the reproducibility errors associated with qDESS T2 is essential to profiling the technical performance of this biomarker.To examine the combined acquisition and segmentation reproducibility of knee cartilage qDESS T2 using two different regional analysis schemes: 1) manual segmentation of subregions loaded during common activities and 2) automatic subregional segmentation.Prospective.11 uninjured participants (age: 28 ± 3 years; 8 (73%) female).3-T, qDESS.Test-retest T2 maps were acquired twice on the same day and with a 1-week interval between scans. For each acquisition, average cartilage T2 was calculated in four manually segmented regions encompassing tibiofemoral contact areas during common activities and 12 automatically segmented regions from the deep-learning open-source framework for musculoskeletal MRI analysis (DOSMA) encompassing medial and lateral anterior, central, and posterior tibiofemoral regions. Test-retest T2 values from matching regions were used to evaluate reproducibility.Coefficients of variation (%CV), root-mean-square-average-CV (%RMSA-CV), and intraclass correlation coefficients (ICCs) assessed test-retest T2 reproducibility. The median of test-retest standard deviations was used for T2 precision. Bland-Altman (BA) analyses examined test-retest biases. The smallest detectable difference (SDD) was defined as the BA limit of agreement of largest magnitude. Significance was accepted for P < 0.05.All cartilage regions across both segmentation schemes demonstrated intraday and interday qDESS T2 CVs and RMSA-CVs of ≤5%. T2 ICC values >0.75 were observed in the majority of regions but were more variable in interday tibial comparisons. Test-retest T2 precision was <1.3 msec. The T2 SDD was 3.8 msec.Excellent CV and RMSA-CV reproducibility may suggest that qDESS T2 increases or decreases >5% (3.8 msec) could represent changes to cartilage composition.Stage 2.

    View details for DOI 10.1002/jmri.29431

    View details for PubMedID 38703134

  • Distortionless, free-breathing, and respiratory resolved 3D diffusion weighted imaging of the abdomen. Magnetic resonance in medicine Lee, P. K., Zhou, X., Wang, N., Syed, A. B., Brunsing, R. L., Vasanawala, S. S., Hargreaves, B. A. 2024

    Abstract

    Abdominal imaging is frequently performed with breath holds or respiratory triggering to reduce the effects of respiratory motion. Diffusion weighted sequences provide a useful clinical contrast but have prolonged scan times due to low signal-to-noise ratio (SNR), and cannot be completed in a single breath hold. Echo-planar imaging (EPI) is the most commonly used trajectory for diffusion weighted imaging but it is susceptible to off-resonance artifacts. A respiratory resolved, three-dimensional (3D) diffusion prepared sequence that obtains distortionless diffusion weighted images during free-breathing is presented. Techniques to address the myriad of challenges including: 3D shot-to-shot phase correction, respiratory binning, diffusion encoding during free-breathing, and robustness to off-resonance are described.A twice-refocused, M1-nulled diffusion preparation was combined with an RF-spoiled gradient echo readout and respiratory resolved reconstruction to obtain free-breathing diffusion weighted images in the abdomen. Cartesian sampling permits a sampling density that enables 3D shot-to-shot phase navigation and reduction of transient fat artifacts. Theoretical properties of a region-based shot rejection are described. The region-based shot rejection method was evaluated with free-breathing (normal and exaggerated breathing), and respiratory triggering. The proposed sequence was compared in vivo with multishot DW-EPI.The proposed sequence exhibits no evident distortion in vivo when compared to multishot DW-EPI, robustness to B0 and B1 field inhomogeneities, and robustness to motion from different respiratory patterns.Acquisition of distortionless, diffusion weighted images is feasible during free-breathing with a b-value of 500 s/mm2, scan time of 6 min, and a clinically viable reconstruction time.

    View details for DOI 10.1002/mrm.30067

    View details for PubMedID 38688875

  • Robust multishot diffusion-weighted imaging of the abdomen with region-based shot rejection. Magnetic resonance in medicine Lee, P. K., Zhou, X., Hargreaves, B. A. 2024

    Abstract

    Diffusion-weighted (DW) imaging provides a useful clinical contrast, but is susceptible to motion-induced dephasing caused by the application of strong diffusion gradients. Phase navigators are commonly used to resolve shot-to-shot motion-induced phase in multishot reconstructions, but poor phase estimates result in signal dropout and Apparent Diffusion Coefficient (ADC) overestimation. These artifacts are prominent in the abdomen, a region prone to involuntary cardiac and respiratory motion. To improve the robustness of DW imaging in the abdomen, region-based shot rejection schemes that selectively weight regions where the shot-to-shot phase is poorly estimated were evaluated.Spatially varying weights for each shot, reflecting both the accuracy of the estimated phase and the degree of subvoxel dephasing, were estimated from the phase navigator magnitude images. The weighting was integrated into a multishot reconstruction using different formulations and phase navigator resolutions and tested with different phase navigator resolutions in multishot DW-echo Planar Imaging acquisitions of the liver and pancreas, using conventional monopolar and velocity-compensated diffusion encoding. Reconstructed images and ADC estimates were compared qualitatively.The proposed region-based shot rejection reduces banding and signal dropout artifacts caused by physiological motion in the liver and pancreas. Shot rejection allows conventional monopolar diffusion encoding to achieve median ADCs in the pancreas comparable to motion-compensated diffusion encoding, albeit with a greater spread of ADCs.Region-based shot rejection is a linear reconstruction that improves the motion robustness of multi-shot DWI and requires no sequence modifications.

    View details for DOI 10.1002/mrm.30102

    View details for PubMedID 38623901

  • Clinical evaluation of isotropic MAVRIC-SL for symptomatic hip arthroplasties at 3 T MRI. Magnetic resonance imaging Yoon, D., Doyle, Z., Lee, P., Hargreaves, B., Stevens, K. 2024

    Abstract

    3D multi-spectral imaging (MSI) of metal implants necessitates relatively long scan times.We implemented a fast isotropic 3D MSI technique at 3 T and compared its image quality and clinical utility to non-isotropic MSI in the evaluation of hip implants.Two musculoskeletal radiologists scored images from coronal proton density-weighted conventional MAVRIC-SL and an isotropic MAVRIC-SL sequence accelerated with robust-component-analysis on a 3-point scale (3: diagnostic, 2: moderately diagnostic, 1: non-diagnostic) for overall image quality, metal artifact, and visualization around femoral and acetabular components. Grades were compared using a signed Wilcoxon test. Images were evaluated for effusion, synovitis, osteolysis, loosening, pseudotumor, fracture, and gluteal tendon abnormalities. Reformatted axial and sagittal images for both sequences were subsequently generated and compared for image quality with the Wilcoxon test. Whether these reformats increased diagnostic confidence or revealed additional pathology, including findings unrelated to arthroplasty that may contribute to hip pain, was also compared using the McNemar test. Inter-rater agreement was measured by Cohen's kappa.39 symptomatic patients with a total of 59 hip prostheses were imaged (mean age, 70 years ±9, 14 males, 25 females). Comparison scores between coronal images showed no significant difference in image quality, metal artifact, or visualization of the femur and acetabulum. Except for loosening, reviewers identified more positive cases of pathology on the original coronally-acquired isotropic sequence. In comparison of reformatted axial and sagittal images, the isotropic sequence scored significantly (p < 0.01) higher for overall image quality (3.0 vs 2.0) and produced significantly (p < 0.01) more cases of increased diagnostic confidence (42.4% vs 7.6%) or additional diagnoses (50.8% vs 22.9%). Inter-rater agreement was substantial (k = 0.798) for image quality. Mean scan times were 4.2 mins (isotropic) and 7.1 mins (non-isotropic).Compared to the non-isotropic sequence, isotropic 3D MSI was acquired in less time while maintaining diagnostically acceptable image quality. It identified more pathology, including postoperative complications and potential pain-generating pathology unrelated to arthroplasty. This fast isotropic 3D MSI sequence demonstrates promise for improving diagnostic evaluation of symptomatic hip prostheses at 3 T while simultaneously reducing scan time.

    View details for DOI 10.1016/j.mri.2024.04.017

    View details for PubMedID 38621551

  • 3D CLUSTERING OF T2 MAPS IDENTIFIES FOCAL CARTILAGE CHANGES FROM 3-WEEKS TO 2-YEARS FOLLOWING ACL RECONSTRUCTION Pai, A. S., Gatti, A. A., Black, M., Young, K., Asay, J., Kogan, F., Sherman, S., Gold, G. E., Hargreaves, B., Chaudhari, A. ELSEVIER SCI LTD. 2024: S360-S361
  • Stereoscopic calibration for augmented reality visualization in microscopic surgery. International journal of computer assisted radiology and surgery El Chemaly, T., Athayde Neves, C., Leuze, C., Hargreaves, B., H Blevins, N. 2023

    Abstract

    Middle and inner ear procedures target hearing loss, infections, and tumors of the temporal bone and lateral skull base. Despite the advances in surgical techniques, these procedures remain challenging due to limited haptic and visual feedback. Augmented reality (AR) may improve operative safety by allowing the 3D visualization of anatomical structures from preoperative computed tomography (CT) scans on real intraoperative microscope video feed. The purpose of this work was to develop a real-time CT-augmented stereo microscope system using camera calibration and electromagnetic (EM) tracking.A 3D printed and electromagnetically tracked calibration board was used to compute the intrinsic and extrinsic parameters of the surgical stereo microscope. These parameters were used to establish a transformation between the EM tracker coordinate system and the stereo microscope image space such that any tracked 3D point can be projected onto the left and right images of the microscope video stream. This allowed the augmentation of the microscope feed of a 3D printed temporal bone with its corresponding CT-derived virtual model. Finally, the calibration board was also used for evaluating the accuracy of the calibration.We evaluated the accuracy of the system by calculating the registration error (RE) in 2D and 3D in a microsurgical laboratory setting. Our calibration workflow achieved a RE of 0.11 ± 0.06 mm in 2D and 0.98 ± 0.13 mm in 3D. In addition, we overlaid a 3D CT model on the microscope feed of a 3D resin printed model of a segmented temporal bone. The system exhibited small latency and good registration accuracy.We present the calibration of an electromagnetically tracked surgical stereo microscope for augmented reality visualization. The calibration method achieved accuracy within a range suitable for otologic procedures. The AR process introduces enhanced visualization of the surgical field while allowing depth perception.

    View details for DOI 10.1007/s11548-023-02980-5

    View details for PubMedID 37450175

    View details for PubMedCentralID 4634572