Hybrid data fidelity term approach for quantitative susceptibility mapping

PURPOSE: Susceptibility maps are usually derived from local magnetic field estimations by minimizing a functional composed of a data consistency term and a regularization term. The data-consistency term measures the difference between the desired solution and the measured data using typically the L2-norm. It has been proposed to replace this L2-norm with the L1-norm, due to its robustness to outliers and reduction of streaking artifacts arising from highly noisy or strongly perturbed regions. However, in regions with high SNR, the L1-norm yields a suboptimal denoising performance. In this work, we present a hybrid data fidelity approach that uses the L1-norm and subsequently the L2-norm to exploit the strengths of both norms. METHODS: We developed a hybrid data fidelity term approach for QSM (HD-QSM) based on linear susceptibility inversion methods, with total variation regularization. Each functional is solved with ADMM. The HD-QSM approach is a two-stage method that first finds a fast solution of the L1-norm functional and then uses this solution to initialize the L2-norm functional. In both norms we included spatially variable weights that improve the quality of the reconstructions. RESULTS: The HD-QSM approach produced good quantitative reconstructions in terms of structural definition, noise reduction, and avoiding streaking artifacts comparable with nonlinear methods, but with higher computational efficiency. Reconstructions performed with this method achieved first place at the lowest RMS error category in stage 1 of the 2019 QSM Reconstruction Challenge. CONCLUSIONS: The proposed method allows robust and accurate QSM reconstructions, obtaining superior performance to state-of-the-art methods

Deep optical images of malin 1 reveal new features

We present Megacam deep optical images (g and r) of Malin 1 obtained with the 6.5m Magellan/Clay telescope, detecting structures down to ~ 28 B mag arcsec-2. In order to enhance galaxy features buried in the noise, we use a noise reduction filter based on the total generalized variation regularizator. This method allows us to detect and resolve very faint morphological features, including spiral arms, with a high visual contrast. For the first time, we can appreciate an optical image of Malin 1 and its morphology in full view. The images provide unprecedented detail, compared to those obtained in the past with photographic plates and CCD, including HST imaging. We detect two peculiar features in the disk/spiral arms. The analysis suggests that the first one is possibly a background galaxy, and the second is an apparent stream without a clear nature, but could be related to the claimed past interaction between Malin 1 and the galaxy SDSSJ123708.91 + 142253.2. Malin 1 exhibits features suggesting the presence of stellar associations, and clumps of molecular gas, not seen before with such a clarity. Using these images, we obtain a diameter for Malin 1 of 160 kpc, ~ 50 kpc larger than previous estimates. A simple analysis shows that the observed spiral arms reach very low luminosity and mass surface densities, to levels much lower than the corresponding values for the Milky WayPreprin

Latin American Collaborative Research on Aplastic Anemia (LARAA): creating a regional registry

Aplastic anemia (AA) is a rare but serious disease that affects hematopoietic stem cells and is characterized by pancytopenia and a hypocellular bone marrow. It can be a hereditary or acquired condition. Acquired AA has an incidence of 2 per million per year in Europe, but the incidence is two to three times higher in Asia. In Latin America, there is little epidemiologic data on this disease. The most important treatments for AA are bone marrow transplantation and immunosuppressive treatment with antithymocyte globulin and cyclosporine. But access to these treatments is restricted in some areas of Latin America. At the American Society of Hematology (ASH) Annual Meeting in 2016, representatives of the Hematology Societies of Latin America, with the support of the ASH International Program, met to discuss possible collaborative efforts. Everyone agreed that lack of reliable information is one of the main barriers to designing significant clinical trials for the region; therefore, starting a registry of hematologic diseases for the region has become a main goal of the group. In April 2017, at the ASH Highlights meeting in Latin America, AA was selected as the first disease that would be used to begin the collaborative action. National hematology societies of Argentina, Bolivia, Brazil, Chile, Colombia, Costa Rica, Paraguay, Peru, Uruguay, and Venezuela have made a commitment to help develop the Latin American Registry for Aplastic Anemia (LARAA)

Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting

The Latin American experience of allografting patients with severe aplastic anaemia: real-world data on the impact of stem cell source and ATG administration in HLA-identical sibling transplants

We studied 298 patients with severe aplastic anaemia (SAA) allografted in four Latin American countries. The source of cells was bone marrow (BM) in 94 patients and PBSCs in 204 patients. Engraftment failed in 8.1% of recipients with no difference between BM and PBSCs (P = 0.08). Incidence of acute GvHD (aGvHD) for BM and PBSCs was 30% vs 32% (P = 0.18), and for grades III–IV was 2.6% vs 11.6% (P = 0.01). Chronic GvHD (cGvHD) between BM and PBSCs was 37% vs 59% (P = 0.002) and extensive 5% vs 23.6% (P = 0.01). OS was 74% vs 76% for BM vs PBSCs (P = 0.95). Event-free survival was superior in patients conditioned with anti-thymocyte globulin (ATG)-based regimens compared with other regimens (79% vs 61%, P = 0.001) as excessive secondary graft failure was seen with other regimens (10% vs 26%, P = 0.005) respectively. In multivariate analysis, aGvHD II–IV (hazard ratio (HR) 2.50, confidence interval (CI) 1.1–5.6, P = 0.02) and aGvHD III–IV (HR 8.3 CI 3.4–20.2, Po0.001) proved to be independent negative predictors of survival. In conclusion, BM as a source of cells and ATG-based regimens should be standard because of higher GvHD incidence with PBSCs, although the latter combining with ATG in the conditioning regimen could be an option in selected high-risk patient

Calcium (Ca2+) waves data calibration and analysis using image processing techniques

BACKGROUND: Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium density and characterizing the traveling wave plays a key role in understanding biological phenomena. However, current methods to measure propagation velocities and other wave characteristics involve several manual or time-consuming procedures. This limits the amount of information that can be extracted, and the statistical quality of the analysis. RESULTS: Our work provides a framework based on image processing procedures that enables a fast, automatic and robust characterization of data from two-filter fluorescence Ca2+ experiments. We calculate the mean velocity of the wave-front, and use theoretical models to extract meaningful parameters like wave amplitude, decay rate and time of excitation. CONCLUSIONS: Measurements done by different operators showed a high degree of reproducibility. This framework is also extended to a single filter fluorescence experiments, allowing higher sampling rates, and thus an increased accuracy in velocity measurements

Comparison of parameter optimization methods for quantitative susceptibility mapping

Purpose: Quantitative Susceptibility Mapping (QSM) is usually performed by minimizing a functional with data fidelity and regularization terms. A weighting parameter controls the balance between these terms. There is a need for techniques to find the proper balance that avoids artifact propagation and loss of details. Finding the point of maximum curvature in the L‐curve is a popular choice, although it is slow, often unreliable when using variational penalties, and has a tendency to yield overregularized results. / Methods: We propose 2 alternative approaches to control the balance between the data fidelity and regularization terms: 1) searching for an inflection point in the log‐log domain of the L‐curve, and 2) comparing frequency components of QSM reconstructions. We compare these methods against the conventional L‐curve and U‐curve approaches. Results Our methods achieve predicted parameters that are better correlated with RMS error, high‐frequency error norm, and structural similarity metric‐based parameter optimizations than those obtained with traditional methods. The inflection point yields less overregularization and lower errors than traditional alternatives. The frequency analysis yields more visually appealing results, although with larger RMS error. / Conclusion: Our methods provide a robust parameter optimization framework for variational penalties in QSM reconstruction. The L‐curve–based zero‐curvature search produced almost optimal results for typical QSM acquisition settings. The frequency analysis method may use a 1.5 to 2.0 correction factor to apply it as a stand‐alone method for a wider range of signal‐to‐noise‐ratio settings. This approach may also benefit from fast search algorithms such as the binary search to speed up the process

Deep optical images of malin 1 reveal new features

We present Megacam deep optical images (g and r) of Malin 1 obtained with the 6.5m Magellan/Clay telescope, detecting structures down to ~ 28 B mag arcsec-2. In order to enhance galaxy features buried in the noise, we use a noise reduction filter based on the total generalized variation regularizator. This method allows us to detect and resolve very faint morphological features, including spiral arms, with a high visual contrast. For the first time, we can appreciate an optical image of Malin 1 and its morphology in full view. The images provide unprecedented detail, compared to those obtained in the past with photographic plates and CCD, including HST imaging. We detect two peculiar features in the disk/spiral arms. The analysis suggests that the first one is possibly a background galaxy, and the second is an apparent stream without a clear nature, but could be related to the claimed past interaction between Malin 1 and the galaxy SDSSJ123708.91 + 142253.2. Malin 1 exhibits features suggesting the presence of stellar associations, and clumps of molecular gas, not seen before with such a clarity. Using these images, we obtain a diameter for Malin 1 of 160 kpc, ~ 50 kpc larger than previous estimates. A simple analysis shows that the observed spiral arms reach very low luminosity and mass surface densities, to levels much lower than the corresponding values for the Milky Wa

QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures

International audienceThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited