Publications

Cerebrospinal fluid partial volume effect is a known bias in the estimation of Diffusion Tensor Imaging (DTI) parameters from diffusion MRI data. The Free-Water Imaging model for diffusion MRI data adds a second compartment to the DTI model, which explicitly accounts for the signal contribution of extracellular free-water, such as cerebrospinal fluid. As a result the DTI parameters obtained through the free-water model are corrected for partial volume effects, and thus better represent tissue microstructure. In addition, the model estimates the fractional volume of free-water, and can be used to monitor changes in the extracellular space. Under certain assumptions, the model can be estimated from single-shell diffusion MRI data. However, by using data from multi-shell diffusion acquisitions, these assumptions can be relaxed, and the fit becomes more robust. Nevertheless, fitting the model to multi-shell data requires high computational cost, with a non-linear iterative minimization, which has to be initialized close enough to the global minimum to avoid local minima and to robustly estimate the model parameters. Here we investigate the properties of the main initialization approaches that are currently being used, and suggest new fast approaches to improve the initial estimates of the model parameters. We show that our proposed approaches provide a fast and accurate initial approximation of the model parameters, which is very close to the final solution. We demonstrate that the proposed initializations improve the final outcome of non-linear model fitting.

PURPOSE: To develop an accelerated, robust, and accurate diffusion MRI acquisition and reconstruction technique for submillimeter whole human brain in vivo scan on a clinical scanner. METHODS: We extend the ultra-high resolution diffusion MRI acquisition technique, gSlider, by allowing undersampling in q-space and radiofrequency (RF)-encoding space, thereby dramatically reducing the total acquisition time of conventional gSlider. The novel method, termed gSlider-SR, compensates for the lack of acquired information by exploiting redundancy in the dMRI data using a basis of spherical ridgelets (SR), while simultaneously enhancing the signal-to-noise ratio. Using Monte Carlo simulation with realistic noise levels and several acquisitions of in vivo human brain dMRI data (acquired on a Siemens Prisma 3T scanner), we demonstrate the efficacy of our method using several quantitative metrics. RESULTS: For high-resolution dMRI data with realistic noise levels (synthetically added), we show that gSlider-SR can reconstruct high-quality dMRI data at different acceleration factors preserving both signal and angular information. With in vivo data, we demonstrate that gSlider-SR can accurately reconstruct 860 μm diffusion MRI data (64 diffusion directions at ), at comparable quality as that obtained with conventional gSlider with four averages, thereby providing an eight-fold reduction in scan time (from 1 hour 20 to 10 minutes). CONCLUSIONS: gSlider-SR enables whole-brain high angular resolution dMRI at a submillimeter spatial resolution with a dramatically reduced acquisition time, making it feasible to use the proposed scheme on existing clinical scanners.

Age-related memory impairments have been linked to differences in structural brain parameters, including cerebral white matter (WM) microstructure and hippocampal (HC) volume, but their combined influences are rarely investigated. In a population-based sample of 337 older participants aged 61-82 years (Mage = 69.66, SDage = 3.92 years), we modeled the independent and joint effects of limbic WM microstructure and HC subfield volumes on verbal learning. Participants completed a verbal learning task of recall over five repeated trials and underwent magnetic resonance imaging (MRI), including structural and diffusion scans. We segmented three HC subregions on high-resolution MRI data and sampled mean fractional anisotropy (FA) from bilateral limbic WM tracts identified via deterministic fiber tractography. Using structural equation modeling, we evaluated the associations between learning rate and latent factors representing FA sampled from limbic WM tracts, and HC subfield volumes, and their latent interaction. Results showed limbic WM and the interaction of HC and WM-but not HC volume alone-predicted verbal learning rates. Model decomposition revealed HC volume is only positively associated with learning rate in individuals with higher WM anisotropy. We conclude that the structural characteristics of limbic WM regions and HC volume jointly contribute to verbal learning in older adults.

BACKGROUND: In previous work, we applied novel in vivo imaging methods to reveal that white matter pathology in patients with first-episode psychosis (FEP) is mainly characterized by excessive extracellular free-water, and to a lesser extent by cellular processes, such as demyelination. Here, we apply a back-translational approach to evaluate whether or not a rodent model of maternal immune activation (MIA) induces patterns of white matter pathology that we observed in patients with FEP. To this end, we examined free-water and tissue-specific white matter alterations in rats born to mothers exposed to the viral mimic polyriboinosinic-polyribocytidylic acid (Poly-I:C) in pregnancy, which is widely used to produce alterations relevant to schizophrenia and is characterized by a robust neuroinflammatory response. METHOD: Pregnant dams were injected on gestational day 15 with the viral mimic Poly-I:C (4 mg/kg) or saline. Diffusion-weighted magnetic resonance images were acquired from 17 male offspring (9 Poly-I:C and 8 saline) on postnatal day 90, after the emergence of brain structural and behavioral abnormalities. The free-water fraction (FW) and tissue-specific fractional anisotropy (FA), as well as conventional fractional anisotropy (FA) were computed across voxels traversing a white matter skeleton. Voxel-wise and whole-brain averaged white matter were tested for significant microstructural alterations in immune-challenged, relative to saline-exposed offspring.

BACKGROUND: Relative enlargement of the pulmonary artery (PA) on chest CT imaging is associated with respiratory exacerbations in patients with COPD or cystic fibrosis. We sought to determine whether similar findings were present in patients with asthma and whether these findings were explained by differences in ventricular size. METHODS: We measured the PA and aorta diameters in 233 individuals from the Severe Asthma Research Program III cohort. We also estimated right, left, and total epicardial cardiac ventricular volume indices (eERVVI, eELVVI, and eETVVI, respectively). Associations between the cardiac and PA measures (PA-to-aorta [PA/A] ratio, eERVVI-to-eELVVI [eRV/eLV] ratio, eERVVI, eELVVI, eETVVI) and clinical measures of asthma severity were assessed by Pearson correlation, and associations with asthma severity and exacerbation rate were evaluated by multivariable linear and zero-inflated negative binomial regression.

The first episode of psychosis is typically preceded by a prodromal phase with subthreshold symptoms and functional decline. Improved outcome prediction in this stage is needed to allow targeted early intervention. This study assesses a combined clinical and resting-state fMRI prediction model in 137 adolescents and young adults at Clinical High Risk (CHR) for psychosis from the Shanghai At Risk for Psychosis (SHARP) program. Based on outcome at one-year follow-up, participants were separated into three outcome categories including good outcome (symptom remission, N = 71), intermediate outcome (ongoing CHR symptoms, N = 30), and poor outcome (conversion to psychosis or treatment-refractory, N = 36). Validated clinical predictors from the psychosis-risk calculator were combined with measures of resting-state functional connectivity. Using multinomial logistic regression analysis and leave-one-out cross-validation, a clinical-only prediction model did not achieve a significant level of outcome prediction (F = 0.32, p = .154). An imaging-only model yielded a significant prediction model (F = 0.41, p = .016), but a combined model including both clinical and connectivity measures showed the best performance (F = 0.46, p 

BACKGROUND: The cingulum bundle (CB) is a major white matter fiber tract of the limbic system that underlies cingulate cortex, passing longitudinally over the corpus callosum. The connectivity of this white matter fiber tract plays a major role in emotional expression, attention, motivation, and working memory, all of which are affected in schizophrenia. Myelin related CB abnormalities have also been implicated in schizophrenia. The purpose of this study is to determine whether or not CB abnormalities are evident in individuals at clinical high risk (CHR) for psychosis, and whether or not cognitive deficits in the domains subserved by CB are related to its structural abnormalities. METHODS: Diffusion Tensor Imaging (DTI) was performed on a 3 T magnet. DT tractography was used to evaluate CB in 20 individuals meeting CHR criteria (13 males/7 females) and 23 healthy controls (12 males/11 females) group matched on age, gender, parental socioeconomic status, education, and handedness. Fractional anisotropy (FA), a measure of white matter coherence and integrity, radial diffusivity (RD), thought to reflect myelin integrity, trace, a possible marker of atrophy, and axial diffusivity (AD), thought to reflect axonal integrity, were averaged over the entire tract and used to investigate CB abnormalities in individuals at CHR for psychosis compared with healthy controls.

The so-called "dot-compartment" is conjectured in diffusion MRI to represent small spherical spaces, such as cell bodies, in which the diffusion is restricted in all directions. Previous investigations inferred its existence from data acquired with directional diffusion encoding which does not permit a straightforward separation of signals from ’sticks’ (axons) and signals from ’dots’. Here we combine isotropic diffusion encoding with ultra-strong diffusion gradients (240 ​mT/m) to achieve high diffusion-weightings with high signal to noise ratio, while suppressing signal arising from anisotropic water compartments with significant mobility along at least one axis (e.g., axons). A dot-compartment, defined to have apparent diffusion coefficient equal to zero and no exchange, would result in a non-decaying signal at very high b-values (b≳7000s/mm). With this unique experimental setup, a residual yet slowly decaying signal above the noise floor for b-values as high as 15000s/mm was seen clearly in the cerebellar grey matter (GM), and in several white matter (WM) regions to some extent. Upper limits of the dot-signal-fraction were estimated to be 1.8% in cerebellar GM and 0.5% in WM. By relaxing the assumption of zero diffusivity, the signal at high b-values in cerebellar GM could be represented more accurately by an isotropic water pool with a low apparent diffusivity of 0.12 μm/ms and a substantial signal fraction of 9.7%. The T2 of this component was estimated to be around 61ms. This remaining signal at high b-values has potential to serve as a novel and simple marker for isotropically-restricted water compartments in cerebellar GM.

In this work we investigate the use of sum of squares constraints for various diffusion-weighted MRI models, with a goal of enforcing strict, global non-negativity of the diffusion propagator. We formulate such constraints for the mean apparent propagator model and for spherical deconvolution, guaranteeing strict non-negativity of the corresponding diffusion propagators. For the cumulant expansion similar constraints cannot exist, and we instead derive a set of auxiliary constraints that are necessary but not sufficient to guarantee non-negativity. These constraints can all be verified and enforced at reasonable computational costs using semidefinite programming. By verifying our constraints on standard reconstructions of the different models, we show that currently used weak constraints are largely ineffective at ensuring non-negativity. We further show that if strict non-negativity is not enforced then estimated model parameters may suffer from significant errors, leading to serious inaccuracies in important derived quantities such as the main fiber orientations, mean kurtosis, etc. Finally, our experiments confirm that the observed constraint violations are mostly due to measurement noise, which is difficult to mitigate and suggests that properly constrained optimization should currently be considered the norm in many cases.