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•We introduce a novel framework to perform spherical deconvolution with multiple anisotropic response functions (mFOD).•We show that the proposed framework can be used to improve the FOD estimation in the cortical gray matter.•Fiber tractography performed with mFOD reaches the cortical GM with more coverage and contiguity than with previous methods.•The proposed framework is a first step towards GM to GM fiber tractography. In diffusion MRI, spherical deconvolution approaches can estimate local white matter (WM) fiber orientation distributions (FOD) which can be used to produce fiber tractography reconstructions. The applicability of spherical deconvolution to gray matter (GM), however, is still limited, despite its critical role as start/endpoint of WM fiber pathways. The advent of multi-shell diffusion MRI data offers additional contrast to model the GM signal but, to date, only isotropic models have been applied to GM. Evidence from both histology and high-resolution diffusion MRI studies suggests a marked anisotropic character of the diffusion process in GM, which could be exploited to improve the description of the cortical organization. In this study, we investigated whether performing spherical deconvolution with tissue specific models of both WM and GM can improve the characterization of the latter while retaining state-of-the-art performances in WM. To this end, we developed a framework able to simultaneously accommodate multiple anisotropic response functions to estimate multiple, tissue-specific, fiber orientation distributions (mFODs). As proof of principle, we used the diffusion kurtosis imaging model to represent the WM signal, and the neurite orientation dispersion and density imaging (NODDI) model to represent the GM signal. The feasibility of the proposed approach is shown with numerical simulations and with data from the Human Connectome Project (HCP). The performance of our method is compared to the current state of the art, multi-shell constrained spherical deconvolution (MSCSD). The simulations show that with our new method we can accurately estimate a mixture of two FODs at SNR≥50. With HCP data, the proposed method was able to reconstruct both tangentially and radially oriented FODs in GM, and performed comparably well to MSCSD in computing FODs in WM. When performing fiber tractography, the trajectories reconstructed with mFODs reached the cortex with more spatial continuity and for a longer distance as compared to MSCSD and allowed to reconstruct short trajectories tangential to the cortical folding. In conclusion, we demonstrated that our proposed method allows to perform spherical deconvolution of multiple anisotropic response functions, specifically improving the performances of spherical deconvolution in GM tissue.

Spherical deconvolution is a widely used approach to quantify the fiber orientation distribution (FOD) from diffusion MRI data of the brain. The damped Richardson-Lucy (dRL) is an algorithm developed to perform robust spherical deconvolution on single-shell diffusion MRI data while suppressing spurious FOD peaks due to noise or partial volume effects. Due to recent progress in acquisition hardware and scanning protocols, it is becoming increasingly common to acquire multi-shell diffusion MRI data, which allows for the modelling of multiple tissue types beyond white matter. While the dRL algorithm could, in theory, be directly applied to multi-shell data, it is not optimised to exploit its information content to model the signal from multiple tissue types. In this work, we introduce a new framework based on dRL – dubbed generalized Richardson-Lucy (GRL) – that uses multi-shell data in combination with user-chosen tissue models to disentangle partial volume effects and increase the accuracy in FOD estimation. Further, GRL estimates signal fraction maps associated to each user-selected model, which can be used during fiber tractography to dissect and terminate the tracking without need for additional structural data. The optimal weighting of multi-shell data in the fit and the robustness to noise and to partial volume effects of GRL was studied with synthetic data. Subsequently, we investigated the performance of GRL in comparison to dRL and to multi-shell constrained spherical deconvolution (MSCSD) on a high-resolution diffusion MRI dataset from the Human Connectome Project and on an MRI dataset acquired at 3T on a clinical scanner. In line with previous studies, we described the signal of the cerebrospinal-fluid and of the grey matter with isotropic diffusion models, whereas four diffusion models were considered to describe the white matter. With a third dataset including small diffusion weightings, we studied the feasibility of including intra-voxel incoherent motion effects due to blood pseudo-diffusion in the modelling. Further, the reliability of GRL was demonstrated with a test-retest scan of a subject acquired at 3T. Results of simulations show that GRL can robustly disentangle different tissue types at SNR above 20 with respect to the non-weighted image, and that it improves the angular accuracy of the FOD estimation as compared to dRL. On real data, GRL provides signal fraction maps that are physiologically plausible and consistent with those obtained with MSCSD, with correlation coefficients between the two methods up to 0.96. When considering IVIM effects, a high blood pseudo-diffusion fraction is observed in the medial temporal lobe and in the sagittal sinus. In comparison to dRL and MSCSD, GRL provided sharper FODs and less spurious peaks in presence of partial volume effects, but the FOD reconstructions are also highly dependent on the chosen modelling of white matter. When performing fiber tractography, GRL allows to terminate fiber tractography using the signal fraction maps, which results in a better tract termination at the grey-white matter interface or at the outer cortical surface. In terms of inter-scan reliability, GRL performed similarly to or better than compared methods. In conclusion, GRL offers a new modular and flexible framework to perform spherical deconvolution of multi-shell data. •A generalized Richardson-Lucy (GRL) method to leverage multi-shell diffusion MRI data.•GRL improves the quality of the WM FOD estimation.•GRL can fit diffusion signals with models of choice – including DTI, DKI and NODDI.•GRL disentangle partial volume effects of WM with GM, CSF and others like IVIM.•GRL uses the signal fraction estimates to terminate the fiber tractography.

•Cardiac-induced 3D brain tissue strain tensor measured using MRI.•Single-shot simultaneous multi-slice DENSE MRI is suitable to acquire tissue strain for voxel-wise assessment.•Strain tensor field is consistent over healthy subjects and has good repeatability.•Brain tissue shows the Poisson effect, where longitudinal expansion is accompanied by transverse compression. The cardiac cycle induces blood volume pulsations in the cerebral microvasculature that cause subtle deformation of the surrounding tissue. These tissue deformations are highly relevant as a potential source of information on the brain's microvasculature as well as of tissue condition. Besides, cyclic brain tissue deformations may be a driving force in clearance of brain waste products. We have developed a high-field magnetic resonance imaging (MRI) technique to capture these tissue deformations with full brain coverage and sufficient signal-to-noise to derive the cardiac-induced strain tensor on a voxel by voxel basis, that could not be assessed non-invasively before. We acquired the strain tensor with 3 mm isotropic resolution in 9 subjects with repeated measurements for 8 subjects. The strain tensor yielded both positive and negative eigenvalues (principle strains), reflecting the Poison effect in tissue. The principle strain associated with expansion followed the known funnel shaped brain motion pattern pointing towards the foramen magnum. Furthermore, we evaluate two scalar quantities from the strain tensor: the volumetric strain and octahedral shear strain. These quantities showed consistent patterns between subjects, and yielded repeatable results: the peak systolic volumetric strain (relative to end-diastolic strain) was 4.19⋅10−4 ± 0.78⋅10−4 and 3.98⋅10−4 ± 0.44⋅10−4 (mean ± standard deviation for first and second measurement, respectively), and the peak octahedral shear strain was 2.16⋅10−3 ± 0.31⋅10−3 and 2.31⋅10−3 ± 0.38⋅10−3, for the first and second measurement, respectively. The volumetric strain was typically highest in the cortex and lowest in the periventricular white matter, while anisotropy was highest in the subcortical white matter and basal ganglia. This technique thus reveals new, regional information on the brain's cardiac-induced deformation characteristics, and has the potential to advance our understanding of the role of microvascular pulsations in health and disease.

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.

Water management is a major contemporary and future challenge. In an increasing water demand scenario related to climate change, a water distribution system must ensure equal access to water for all users. In this context, a reliable short-term water demand forecasting system is crucial for reliable water management. However, despite the abundance of studies in the scientific literature, few examples highlight complete tools for providing such models to real water utilities and water managers. This study presents AI-Forecast, an innovative tool developed to predict water demand with state-of-the-art models. Such tool is based on the data-driven logic, and it is designed to provide a complete data-driven chain that starts from the data and arrives to the short-term water demand prediction. AI-Forecast can import data, properly manage them, and assess tasks like outlier detection and missing data imputation. Eventually, it can implement state-of-the-art forecasting models and provide the forecasts. The prediction is shown through an intuitive web interface, which is designed to highlight the major information related to the prediction accuracy. Although this tool does not provide a new prediction algorithm, it proposes a complete data-driven chain that is practically designed to take such models in practice to real water utilities.

Quantification methods based on the acquisition of diffusion magnetic resonance imaging (dMRI) with multiple diffusion weightings (e.g., multi-shell) are becoming increasingly applied to study the in-vivo brain. Compared to single-shell data for diffusion tensor imaging (DTI), multi-shell data allows to apply more complex models such as diffusion kurtosis imaging (DKI), which attempts to capture both diffusion hindrance and restriction effects, or biophysical models such as NODDI, which attempt to increase specificity by separating biophysical components. Because of the strong dependence of the dMRI signal on the measurement hardware, DKI and NODDI metrics show scanner and site differences, much like other dMRI metrics. These effects limit the implementation of multi-shell approaches in multicenter studies, which are needed to collect large sample sizes for robust analyses. Recently, a post-processing technique based on rotation invariant spherical harmonics (RISH) features was introduced to mitigate cross-scanner differences in DTI metrics. Unlike statistical harmonization methods, which require repeated application to every dMRI metric of choice, RISH harmonization is applied once on the raw data, and can be followed by any analysis. RISH features harmonization has been tested on DTI features but not its generalizability to harmonize multi-shell dMRI. In this work, we investigated whether performing the RISH features harmonization of multi-shell dMRI data removes cross-site differences in DKI and NODDI metrics while retaining longitudinal effects. To this end, 46 subjects underwent a longitudinal (up to 3 time points) two-shell dMRI protocol at 3 imaging sites. DKI and NODDI metrics were derived before and after harmonization and compared both at the whole brain level and at the voxel level. Then, the harmonization effects on cross-sectional and on longitudinal group differences were evaluated. RISH features averaged for each of the 3 sites exhibited prominent between-site differences in the frontal and posterior part of the brain. Statistically significant differences in fractional anisotropy, mean diffusivity and mean kurtosis were observed both at the whole brain and voxel level between all the acquisition sites before harmonization, but not after. The RISH method also proved effective to harmonize NODDI metrics, particularly in white matter. The RISH based harmonization maintained the magnitude and variance of longitudinal changes as compared to the non-harmonized data of all considered metrics. In conclusion, the application of RISH feature based harmonization to multi-shell dMRI data can be used to remove cross-site differences in DKI metrics and NODDI analyses, while retaining inherent relations between longitudinal acquisitions.

Diffusion tensor imaging (DTI) and diffusion kurtosis imaging (DKI) can quantify indices related to brain structure and their change in pathology. However, only few studies have applied these techniques to spinal cord injury (SCI), and subtle microstructural changes in the brain of SCI individuals are not well understood. Our goal was to investigate structural changes in the brain using DTI (fractional anisotropy, FA; mean diffusivity, MD) and DKI parameters (kurtosis anisotropy, KA; mean kurtosis, MK) in subacute SCI and to study whether these changes were associated with clinical outcomes. Twenty-eight individuals with SCI underwent brain MRI 3 months post-injury, alongside 20 healthy controls. Imaging included a multi-shell diffusion protocol, from which DTI and DKI metrics (FA, MD, KA and MK) were derived. Group comparisons were conducted for each metric across 17 brain regions selected based on their relevance to SCI from previous studies. Multiple comparison corrections were applied per metric to account for the number of examined regions. Effect sizes were calculated using Cohen's . For regions showing significant group differences, Spearman correlations were performed to assess associations between imaging metrics and clinical outcomes, including neurological status (ISNCSCI) and functional independence (SCIM III), with correction for multiple comparisons. MD was significantly higher in the right genu of the corpus callosum in the SCI group (adjusted  = 0.021). In this region, MD negatively correlated with SCIM scores (  = -0.51,  = 0.022), whereas MK showed a positive correlation (  = 0.482,  = 0.038). Structural changes in the corpus callosum may reflect impaired interhemispheric communication, linked to reduced functional independence after SCI. DTI and DKI could serve as complementary tools for identifying brain-based biomarkers, potentially informing recovery trajectories.

Purpose Aim of this study is to compare Quantitative Magnetic Resonance Imaging (qMRI) measures between Becker Muscular Dystrophy (BMD) and Healthy Subjects (HS) and to correlate these parameters with clinical scores. Methods Ten BMD patients (mean age ±standard deviation: 38.7 ± 15.0 years) and ten age-matched HS, were investigated through magnetic resonance imaging (MRI) at thigh and calf levels, including: 1) a standard axial T1-weighted sequence; 2) a volumetric T2-weighted sequence; 3) a multiecho spin-echo sequence; 4) a 2-point Dixon sequence; 5) a Diffusion Tensor Imaging (DTI) sequence. Results Mean Fat Fraction (FF), T2-relaxation time and Fractional Anisotropy (FA) DTI at thigh and calf levels were significantly higher in BMD patients than in HS ( p -values < 0.01). FF at thigh and calf levels significantly correlated with North Star Ambulatory Assessment (NSAA) score ( p -values < 0.01) and6 Minutes Walking Test (6MWT) ( p -values < 0.01), whereas only calf muscle FF was significantly associated with time to get up from floor ( p -value = 0.01). T2 significantly correlated with NSAA score ( p -value < 0.01), 6MWT ( p -value = 0.02) and time to get up from floor ( p -value < 0.01) only at calf level. Among DTI values, only FA in thigh and calf muscles significantly correlated with NSAA score, 6MWT and 10-m walk (all p -values < 0.05); only FA in calf muscles significantly correlated with time to get up from floor ( p  = 0.01). Conclusions Muscle FF, T2-relaxometry and DTI, seem to be a promising biomarker to assess BMD disease severity, although further studies are needed to evaluate changes over the time.

PurposeDiffusion-weighted MRI is a promising technique to monitor response to treatment in pediatric rhabdomyosarcoma. However, its validation in clinical practice remains challenging. This study aims to investigate how the tumor segmentation strategy can affect the apparent diffusion coefficient (ADC) measured in pediatric rhabdomyosarcoma.Materials and methodsA literature review was performed in PubMed using search terms relating to MRI and sarcomas to identify commonly applied segmentation strategies. Seventy-six articles were included, and their presented segmentation methods were evaluated. Commonly reported segmentation strategies were then evaluated on diffusion-weighted imaging of five pediatric rhabdomyosarcoma patients to assess their impact on ADC.ResultsWe found that studies applied different segmentation strategies to define the shape of the region of interest (ROI)(outline 60%, circular ROI 27%), to define the segmentation volume (2D 44%, multislice 9%, 3D 21%), and to define the segmentation area (excludes edge 7%, excludes other region 19%, specific area 27%, whole tumor 48%). In addition, details of the segmentation strategy are often unreported. When implementing and comparing these strategies on in-house data, we found that excluding necrotic, cystic, and hemorrhagic areas from segmentations resulted in on average 5.6% lower mean ADC. Additionally, the slice location used in 2D segmentation methods could affect ADC by as much as 66%.ConclusionDiffusion-weighted MRI studies in pediatric sarcoma currently employ a variety of segmentation methods. Our study shows that different segmentation strategies can result in vastly different ADC measurements, highlighting the importance to further investigate and standardize segmentation.Key pointsStrategies for segmenting sarcoma tumors vary widely throughout literature.Details of the segmentation strategy are often not reported.Including necrotic or cystic areas in the segmentation affects diffusion measurements.Varying the slice of a single-slice segmentation can drastically impact diffusion measurements.