FastMRI Prostate: A Publicly Available, Biparametric MRI Dataset to Advance Machine Learning for Prostate Cancer Imaging

The fastMRI brain and knee dataset has enabled significant advances in exploring reconstruction methods for improving speed and image quality for Magnetic Resonance Imaging (MRI) via novel, clinically relevant reconstruction approaches. In this study, we describe the April 2023 expansion of the fastMRI dataset to include biparametric prostate MRI data acquired on a clinical population. The dataset consists of raw k-space and reconstructed images for T2-weighted and diffusion-weighted sequences along with slice-level labels that indicate the presence and grade of prostate cancer. As has been the case with fastMRI, increasing accessibility to raw prostate MRI data will further facilitate research in MR image reconstruction and evaluation with the larger goal of improving the utility of MRI for prostate cancer detection and evaluation. The dataset is available at https://fastmri.med.nyu.edu.Comment: 4 pages, 1 figur

Electron-phonon interaction contribution to the total energy of group IV semiconductor polymorphs: evaluation and implications

In density functional theory (DFT) based total energy studies, the van der Waals (vdW) and zero-point vibrational energy (ZPVE) correction terms are included to obtain energy differences between polymorphs. We introduce a new correction term, due to electron-phonon interactions (EPI). We rely on Allen's general formalism, which goes beyond the Quasi-Harmonic Approximation (QHA), to include the free energy contributions due to quasiparticle interactions. We show that, for semiconductors and insulators, the EPI contributions to the free energies of electrons and phonons are constant terms. Using Allen's formalism in combination with the Allen-Heine theory for EPI corrections, we calculate the zero-point EPI corrections to the total energy for cubic and hexagonal polytypes of Carbon, Silicon and Silicon Carbide. The EPI corrections alter the energy differences between polytypes. In SiC polytypes, the EPI correction term is more sensitive to crystal structure than the vdW and ZPVE terms and is thus essential in determining their energy differences. It clearly establishes that the cubic SiC-3C is metastable and hexagonal SiC-4H is the stable polytype. Our results are consistent with the experimental results of Kleykamp. Our study enables the inclusion of EPI corrections as a separate term in the free energy expression. This opens the way to beyond the QHA by including the contribution of EPI on all thermodynamic properties.Comment: Submitted for publication. 32 pages and 2 figure

The International Workshop on Osteoarthritis Imaging Knee MRI Segmentation Challenge: A Multi-Institute Evaluation and Analysis Framework on a Standardized Dataset

Purpose: To organize a knee MRI segmentation challenge for characterizing the semantic and clinical efficacy of automatic segmentation methods relevant for monitoring osteoarthritis progression. Methods: A dataset partition consisting of 3D knee MRI from 88 subjects at two timepoints with ground-truth articular (femoral, tibial, patellar) cartilage and meniscus segmentations was standardized. Challenge submissions and a majority-vote ensemble were evaluated using Dice score, average symmetric surface distance, volumetric overlap error, and coefficient of variation on a hold-out test set. Similarities in network segmentations were evaluated using pairwise Dice correlations. Articular cartilage thickness was computed per-scan and longitudinally. Correlation between thickness error and segmentation metrics was measured using Pearson's coefficient. Two empirical upper bounds for ensemble performance were computed using combinations of model outputs that consolidated true positives and true negatives. Results: Six teams (T1-T6) submitted entries for the challenge. No significant differences were observed across all segmentation metrics for all tissues (p=1.0) among the four top-performing networks (T2, T3, T4, T6). Dice correlations between network pairs were high (>0.85). Per-scan thickness errors were negligible among T1-T4 (p=0.99) and longitudinal changes showed minimal bias (<0.03mm). Low correlations (<0.41) were observed between segmentation metrics and thickness error. The majority-vote ensemble was comparable to top performing networks (p=1.0). Empirical upper bound performances were similar for both combinations (p=1.0). Conclusion: Diverse networks learned to segment the knee similarly where high segmentation accuracy did not correlate to cartilage thickness accuracy. Voting ensembles did not outperform individual networks but may help regularize individual models.Comment: Submitted to Radiology: Artificial Intelligence; Fixed typo

Strategies in MR-guided focused ultrasound

PurposeTo determine under-sampled k-space gradient echo trajectories for MR thermometry with PRF shift to increase acquisition speed while maintaining temperature accuracy.MethodsA computer simulation was built and used to study the behaviour of temperature measurement errors as different lines of k-space were acquired. A fully acquired k-space was constructed from the information in the Bioheat Transfer Equation (BHTE), various k-space under-sampling schemes were employed and temperature maps were reconstructed using the PRF shift method as a basis. Temperature errors were calculated as the difference in the maximum temperature predicted by the BHTE and the maximum temperature measured by the under-sampled scheme. ResultsUnder-sampled gradient echo keyhole trajectories showed promising results for making temperature measurements. Using 5 interleaves with a 63 keyhole size estimates temperature with only a 0.4% error while providing a 1.68x faster frame rate.ConclusionGradient echo keyhole trajectories can be used to make temperature measurements for MR thermometry with PRF shift. This method can also be applied for shorter sonications and making temperature estimates for multiple slices

Principal Component Analysis of Simultaneous PET‐MRI Reveals Patterns of Bone–Cartilage Interactions in Osteoarthritis

BackgroundBone-cartilage interactions have been implicated in causing osteoarthritis (OA).PurposeTo use [18 F]-NaF PET-MRI to 1) develop automatic image processing code in MatLab to create a model of bone-cartilage interactions and 2) find associations of bone-cartilage interactions with known manifestations of OA.Study typeProspective study aimed to evaluate a data analysis method.PopulationTwenty-nine patients with knee pain or joint stiffness.Field strength/sequence3T MRI (GE), 3D CUBE FSE, 3D combined T1 ρ/T2 MAPSS, [18F]-sodium fluoride, SIGNA TOF (OSEM).AssessmentCorrelation between MRI (cartilage) and PET (bone) quantitative parameters, bone-cartilage interactions model described by modes of variation as derived by principal component analysis (PCA), WORMS scoring on cartilage lesions, bone marrow abnormalities, subchondral cysts.Statistical testsLinear regression, Pearson correlation.ResultsMode 1 was a positive predictor of the bone abnormality score (P = 0.0003, P = 0.001, P = 0.0007) and the cartilage lesion score (P = 0.03, P = 0.01, P = 0.02) in the femur, tibia, and patella, respectively. For the cartilage lesion scores, mode 5 was the most important positive predictor in the femur (P = 3.9E-06), and mode 2 were predictors, significant negative predictor in the tibia (P = 0.007). In the patella, mode 1 was a significant positive predictor of the bone abnormality score (P = 0.0007).Data conclusionBy successfully building an automatic code to create a bone-cartilage interface, we were able to observe dynamic relationships between biochemical changes in the cartilage accompanied with bone remodeling, extended to the whole knee joint instead of simple colocalized observations, shedding light on the interactions that occur between bone and cartilage in OA. Evidence Level: 3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2020;52:1462-1474

Principal Component Analysis of Simultaneous PET‐MRI Reveals Patterns of Bone–Cartilage Interactions in Osteoarthritis

BackgroundBone-cartilage interactions have been implicated in causing osteoarthritis (OA).PurposeTo use [18 F]-NaF PET-MRI to 1) develop automatic image processing code in MatLab to create a model of bone-cartilage interactions and 2) find associations of bone-cartilage interactions with known manifestations of OA.Study typeProspective study aimed to evaluate a data analysis method.PopulationTwenty-nine patients with knee pain or joint stiffness.Field strength/sequence3T MRI (GE), 3D CUBE FSE, 3D combined T1 ρ/T2 MAPSS, [18F]-sodium fluoride, SIGNA TOF (OSEM).AssessmentCorrelation between MRI (cartilage) and PET (bone) quantitative parameters, bone-cartilage interactions model described by modes of variation as derived by principal component analysis (PCA), WORMS scoring on cartilage lesions, bone marrow abnormalities, subchondral cysts.Statistical testsLinear regression, Pearson correlation.ResultsMode 1 was a positive predictor of the bone abnormality score (P = 0.0003, P = 0.001, P = 0.0007) and the cartilage lesion score (P = 0.03, P = 0.01, P = 0.02) in the femur, tibia, and patella, respectively. For the cartilage lesion scores, mode 5 was the most important positive predictor in the femur (P = 3.9E-06), and mode 2 were predictors, significant negative predictor in the tibia (P = 0.007). In the patella, mode 1 was a significant positive predictor of the bone abnormality score (P = 0.0007).Data conclusionBy successfully building an automatic code to create a bone-cartilage interface, we were able to observe dynamic relationships between biochemical changes in the cartilage accompanied with bone remodeling, extended to the whole knee joint instead of simple colocalized observations, shedding light on the interactions that occur between bone and cartilage in OA. Evidence Level: 3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2020;52:1462-1474

Magnetization‐prepared spoiled gradient‐echo snapshot imaging for efficient measurement of R2‐R1ρ in knee cartilage

PurposeTo validate the potential of quantifying R2 -R1ρ using one pair of signals with T1ρ preparation and T2 preparation incorporated to magnetization-prepared angle-modulated partitioned k-space spoiled gradient-echo snapshots (MAPSS) acquisition and to find an optimal preparation time (Tprep ) for in vivo knee MRI.MethodsBloch equation simulations were first performed to assess the accuracy of quantifying R2 -R1ρ using T1ρ - and T2 -prepared signals with an equivalent Tprep . For validation of this technique in comparison to the conventional approach that calculates R2 -R1ρ after estimating both T2 and T1ρ , phantom experiments and in vivo validation with five healthy subjects and five osteoarthritis patients were performed at a clinical 3T scanner.ResultsBloch equation simulations demonstrated that the accuracy of this efficient R2 -R1ρ quantification method and the optimal Tprep can be affected by image signal-to-noise ratio (SNR) and tissue relaxation times, but quantification can be closest to the reference with an around 25 ms Tprep for knee cartilage. Phantom experiments demonstrated that the proposed method can depict R2 -R1ρ changes with agarose gel concentration. With in vivo data, significant correlation was observed between cartilage R2 -R1ρ measured from the conventional and the proposed methods, and a Tprep of 25.6&nbsp;ms provided the most agreement by Bland-Altman analysis. R2 -R1ρ was significantly lower in patients than in healthy subjects for most cartilage compartments.ConclusionAs a potential biomarker to indicate cartilage degeneration, R2 -R1ρ can be efficiently measured using one pair of T1ρ -prepared and T2 -prepared signals with an optimal Tprep considering cartilage relaxation times and image SNR