Publications

2019
Hamoda HM, Makhlouf AT, Fitzsimmons J, Rathi Y, Makris N, Mesholam-Gately RI, Wojcik JD, Goldstein J, McCarley RW, Seidman LJ, et al. Abnormalities in thalamo-cortical connections in patients with first-episode schizophrenia: a two-tensor tractography study. Brain Imaging Behav. 2019;13 (2) :472-481.Abstract
The "cognitive dysmetria" hypothesis suggests that impairments in cognition and behavior in patients with schizophrenia can be explained by disruptions in the cortico-cerebellar-thalamic-cortical circuit. In this study we examine thalamo-cortical connections in patients with first-episode schizophrenia (FESZ). White matter pathways are investigated that connect the thalamus with three frontal cortex regions including the anterior cingulate cortex (ACC), ventrolateral prefrontal cortex (VLPFC), and lateral oribitofrontal cortex (LOFC). We use a novel method of two-tensor tractography in 26 patients with FESZ compared to 31 healthy controls (HC), who did not differ on age, sex, or education. Dependent measures were fractional anisotropy (FA), Axial Diffusivity (AD), and Radial Diffusivity (RD). Subjects were also assessed using clinical functioning measures including the Global Assessment of Functioning (GAF) Scale, the Global Social Functioning Scale (GF: Social), and the Global Role Functioning Scale (GF: Role). FESZ patients showed decreased FA in the right thalamus-right ACC and right-thalamus-right LOFC pathways compared to healthy controls (HCs). In the right thalamus-right VLPFC tract, we found decreased FA and increased RD in the FESZ group compared to HCs. After correcting for multiple comparisons, reductions in FA in the right thalamus- right ACC and the right thalamus- right VLPC tracts remained significant. Moreover, reductions in FA were significantly associated with lower global functioning scores as well as lower social and role functioning scores. We report the first diffusion tensor imaging study of white matter pathways connecting the thalamus to three frontal regions. Findings of white matter alterations and clinical associations in the thalamic-cortical component of the cortico-cerebellar-thalamic-cortical circuit in patients with FESZ support the cognitive dysmetria hypothesis and further suggest the possible involvement of myelin sheath pathology and axonal membrane disruption in the pathogenesis of the disorder.
Lyall AE, Savadjiev P, Del Re EC, Seitz J, O'Donnell LJ, Westin C-F, Mesholam-Gately RI, Petryshen T, Wojcik JD, Nestor P, et al. Utilizing Mutual Information Analysis to Explore the Relationship Between Gray and White Matter Structural Pathologies in Schizophrenia. Schizophr Bull. 2019;45 (2) :386-395.Abstract
Schizophrenia has been characterized as a neurodevelopmental disorder, with structural brain abnormalities reported at all stages. However, at present, it remains unclear whether gray and white matter abnormalities represent related or independent pathologies in schizophrenia. In this study, we present findings from an integrative analysis exploring the morphological relationship between gray and white matter in 45 schizophrenia participants and 49 healthy controls. We utilized mutual information (MI), a measure of how much information two variables share, to assess the morphological dependence between gray and white matter in three segments of the corpus callsoum, and the gray matter regions these segments connect: (1) the genu and the left and right rostral middle frontal gyrus (rMFG), (2) the isthmus and the left and right superior temporal gyrus (STG), (3) the splenium and the left and right lateral occipital gyrus (LOG). We report significantly reduced MI between white matter tract dispersion of the right hemispheric callosal connections to the STG and both cortical thickness and area in the right STG in schizophrenia patients, despite a lack of group differences in cortical thickness, surface area, or dispersion. We believe that this reduction in morphological dependence between gray and white matter may reflect a possible decoupling of the developmental processes that shape morphological features of white and gray matter early in life. The present study also demonstrates the importance of studying the relationship between gray and white matter measures, as opposed to restricting analyses to gray and white matter measures independently.
Alexander DC, Dyrby TB, Nilsson M, Zhang H. Imaging brain microstructure with diffusion MRI: practicality and applications. NMR Biomed. 2019;32 (4) :e3841.Abstract
This article gives an overview of microstructure imaging of the brain with diffusion MRI and reviews the state of the art. The microstructure-imaging paradigm aims to estimate and map microscopic properties of tissue using a model that links these properties to the voxel scale MR signal. Imaging techniques of this type are just starting to make the transition from the technical research domain to wide application in biomedical studies. We focus here on the practicalities of both implementing such techniques and using them in applications. Specifically, the article summarizes the relevant aspects of brain microanatomy and the range of diffusion-weighted MR measurements that provide sensitivity to them. It then reviews the evolution of mathematical and computational models that relate the diffusion MR signal to brain tissue microstructure, as well as the expanding areas of application. Next we focus on practicalities of designing a working microstructure imaging technique: model selection, experiment design, parameter estimation, validation, and the pipeline of development of this class of technique. The article concludes with some future perspectives on opportunities in this topic and expectations on how the field will evolve in the short-to-medium term.
2018
Pasternak O, Kelly S, Sydnor VJ, Shenton ME. Advances in microstructural diffusion neuroimaging for psychiatric disorders. Neuroimage. 2018;182 :259-282.Abstract
Understanding the neuropathological underpinnings of mental disorders such as schizophrenia, major depression, and bipolar disorder is an essential step towards the development of targeted treatments. Diffusion MRI studies utilizing the diffusion tensor imaging (DTI) model have been extremely successful to date in identifying microstructural brain abnormalities in individuals suffering from mental illness, especially in regions of white matter, although identified abnormalities have been biologically non-specific. Building on DTI's success, in recent years more advanced diffusion MRI methods have been developed and applied to the study of psychiatric populations, with the aim of offering increased sensitivity to subtle neurological abnormalities, as well as improved specificity to candidate pathologies such as demyelination and neuroinflammation. These advanced methods, however, usually come at the cost of prolonged imaging sequences or reduced signal to noise, and they are more difficult to evaluate compared with the more simplified approach taken by the now common DTI model. To date, a limited number of advanced diffusion MRI methods have been employed to study schizophrenia, major depression and bipolar disorder populations. In this review we survey these studies, compare findings across diverse methods, discuss the main benefits and limitations of the different methods, and assess the extent to which the application of more advanced diffusion imaging approaches has led to novel and transformative information with regards to our ability to better understand the etiology and pathology of mental disorders.
Bodduluri S, Puliyakote AKS, Gerard SE, Reinhardt JM, Hoffman EA, Newell JD, Nath HP, Han MLK, Washko GR, San José Estépar R, et al. Airway fractal dimension predicts respiratory morbidity and mortality in COPD. J Clin Invest. 2018.Abstract
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized by airway remodeling. Characterization of airway changes on computed tomography has been challenging due to the complexity of the recurring branching patterns, and this can be better measured using fractal dimensions. METHODS: We analyzed segmented airway trees of 8,135 participants enrolled in the COPDGene cohort. The fractal complexity of the segmented airway tree was measured by the Airway Fractal Dimension (AFD) using the Minkowski-Bougliand box-counting dimension. We examined associations between AFD and lung function and respiratory morbidity using multivariable regression analyses. We further estimated the extent of peribronchial emphysema (%) within 5 mm of the airway tree, as this is likely to affect AFD. We classified participants into 4 groups based on median AFD, percentage of peribronchial emphysema, and estimated survival. RESULTS: AFD was significantly associated with forced expiratory volume in one second (FEV1; P < 0.001) and FEV1/forced vital capacity (FEV1/FVC; P < 0.001) after adjusting for age, race, sex, smoking status, pack-years of smoking, BMI, CT emphysema, air trapping, airway thickness, and CT scanner type. On multivariable analysis, AFD was also associated with respiratory quality of life and 6-minute walk distance, as well as exacerbations, lung function decline, and mortality on longitudinal follow-up. We identified a subset of participants with AFD below the median and peribronchial emphysema above the median who had worse survival compared with participants with high AFD and low peribronchial emphysema (adjusted hazards ratio [HR]: 2.72; 95% CI: 2.20-3.35; P < 0.001), a substantial number of whom were not identified by traditional spirometry severity grades. CONCLUSION: Airway fractal dimension as a measure of airway branching complexity and remodeling in smokers is associated with respiratory morbidity and lung function change, offers prognostic information additional to traditional CT measures of airway wall thickness, and can be used to estimate mortality risk. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT00608764. FUNDING: This study was supported by NIH K23 HL133438 (SPB) and the COPDGene study (NIH Grant Numbers R01 HL089897 and R01 HL089856). The COPDGene project is also supported by the COPD Foundation through contributions made to an Industry Advisory Board comprised of AstraZeneca, Boehringer Ingelheim, Novartis, Pfizer, Siemens, Sunovion and GlaxoSmithKline.
Ottino-González J, Jurado MA, García-García I, Segura B, Marqués-Iturria I, Sender-Palacios MJ, Tor E, Prats-Soteras X, Caldú X, Junqué C, et al. Allostatic load and disordered white matter microstructure in overweight adults. Sci Rep. 2018;8 (1) :15898.Abstract
Overweight and stress are both related to brain structural abnormalities. The allostatic load model states that frequent disruption of homeostasis is inherently linked to oxidative stress and inflammatory responses that in turn can damage the brain. However, the effects of the allostatic load on the central nervous system remain largely unknown. The current study aimed to assess the relationship between the allostatic load and the composition of whole-brain white matter tracts in overweight subjects. Additionally, we have also tested for grey matter changes regarding allostatic load increase. Thirty-one overweight-to-obese adults and 21 lean controls participated in the study. Our results showed that overweight participants presented higher allostatic load indexes. Such increases correlated with lower fractional anisotropy in the inferior fronto-occipital fasciculi and the right anterior corona radiata, as well as with grey matter reductions in the left precentral gyrus, the left lateral occipital gyrus, and the right pars opercularis. These results suggest that an otherwise healthy overweight status is linked to long-term biological changes potentially harmful to the brain.
Zhang F, Wu Y, Norton I, Rigolo L, Rathi Y, Makris N, O'Donnell LJ. An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. Neuroimage. 2018;179 :429-447.Abstract
This work presents an anatomically curated white matter atlas to enable consistent white matter tract parcellation across different populations. Leveraging a well-established computational pipeline for fiber clustering, we create a tract-based white matter atlas including information from 100 subjects. A novel anatomical annotation method is proposed that leverages population-based brain anatomical information and expert neuroanatomical knowledge to annotate and categorize the fiber clusters. A total of 256 white matter structures are annotated in the proposed atlas, which provides one of the most comprehensive tract-based white matter atlases covering the entire brain to date. These structures are composed of 58 deep white matter tracts including major long range association and projection tracts, commissural tracts, and tracts related to the brainstem and cerebellar connections, plus 198 short and medium range superficial fiber clusters organized into 16 categories according to the brain lobes they connect. Potential false positive connections are annotated in the atlas to enable their exclusion from analysis or visualization. In addition, the proposed atlas allows for a whole brain white matter parcellation into 800 fiber clusters to enable whole brain connectivity analyses. The atlas and related computational tools are open-source and publicly available. We evaluate the proposed atlas using a testing dataset of 584 diffusion MRI scans from multiple independently acquired populations, across genders, the lifespan (1 day-82 years), and different health conditions (healthy control, neuropsychiatric disorders, and brain tumor patients). Experimental results show successful white matter parcellation across subjects from different populations acquired on multiple scanners, irrespective of age, gender or disease indications. Over 99% of the fiber tracts annotated in the atlas were detected in all subjects on average. One advantage in terms of robustness is that the tract-based pipeline does not require any cortical or subcortical segmentations, which can have limited success in young children and patients with brain tumors or other structural lesions. We believe this is the first demonstration of consistent automated white matter tract parcellation across the full lifespan from birth to advanced age.
Kubicki M, Lyall AE. Antipsychotics and Their Impact on Cerebral White Matter: Part of the Problem or Part of the Solution?. Am J Psychiatry. 2018;175 (11) :1056-1057.
Giancardo L, Sánchez-Ferro A, Arroyo-Gallego T, Butterworth I, Mendoza CS, Montero P, Matarazzo M, Obeso JA, Gray ML, Estépar SJR. Author Correction: Computer keyboard interaction as an indicator of early Parkinson's disease. Sci Rep. 2018;8 (1) :15227.Abstract
A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Sawyer KS, Maleki N, Papadimitriou G, Makris N, Oscar-Berman M, Harris GJ. Cerebral white matter sex dimorphism in alcoholism: a diffusion tensor imaging study. Neuropsychopharmacology. 2018;43 (9) :1876-1883.Abstract
Excessive alcohol consumption is associated with brain aberrations, including abnormalities in frontal and limbic brain regions. In a prior diffusion tensor magnetic resonance imaging (dMRI) study of neuronal circuitry connecting the frontal lobes and limbic system structures, we demonstrated decreases in white matter fractional anisotropy in abstinent alcoholic men. In the present study, we examined sex differences in alcoholism-related abnormalities of white matter connectivity and their association with alcoholism history. The dMRI scans were acquired from 49 abstinent alcoholic individuals (26 women) and 41 nonalcoholic controls (22 women). Tract-based spatial statistical tools were used to estimate regional FA of white matter tracts and to determine sex differences and their relation to measures of alcoholism history. Sex-related differences in white matter connectivity were observed in association with alcoholism: Compared to nonalcoholic men, alcoholic men had diminished FA in portions of the corpus callosum, the superior longitudinal fasciculi II and III, and the arcuate fasciculus and extreme capsule. In contrast, alcoholic women had higher FA in these regions. Sex differences also were observed for correlations between corpus callosum FA and length of sobriety. Our results suggest that sexual dimorphism in white matter microstructure in abstinent alcoholics may implicate underlying differences in the neurobehavioral liabilities for developing alcohol abuse disorders, or for sequelae following abuse.
Hayden LP, Cho MH, Raby BA, Beaty TH, Silverman EK, Hersh CP. Childhood asthma is associated with COPD and known asthma variants in COPDGene: a genome-wide association study. Respir Res. 2018;19 (1) :209.Abstract
BACKGROUND: Childhood asthma is strongly influenced by genetics and is a risk factor for reduced lung function and chronic obstructive pulmonary disease (COPD) in adults. This study investigates self-reported childhood asthma in adult smokers from the COPDGene Study. We hypothesize that childhood asthma is associated with decreased lung function, increased risk for COPD, and that a genome-wide association study (GWAS) will show association with established asthma variants. METHODS: We evaluated current and former smokers ages 45-80 of non-Hispanic white (NHW) or African American (AA) race. Childhood asthma was defined by self-report of asthma, diagnosed by a medical professional, with onset at < 16 years or during childhood. Subjects with a history of childhood asthma were compared to those who never had asthma based on lung function, development of COPD, and genetic variation. GWAS was performed in NHW and AA populations, and combined in meta-analysis. Two sets of established asthma SNPs from published literature were examined for association with childhood asthma. RESULTS: Among 10,199 adult smokers, 730 (7%) reported childhood asthma and 7493 (73%) reported no history of asthma. Childhood asthmatics had reduced lung function and increased risk for COPD (OR 3.42, 95% CI 2.81-4.18). Genotype data was assessed for 8031 subjects. Among NHWs, 391(7%) had childhood asthma, and GWAS identified one genome-wide significant association in KIAA1958 (rs59289606, p = 4.82 × 10). Among AAs, 339 (12%) had childhood asthma. No SNPs reached genome-wide significance in the AAs or in the meta-analysis combining NHW and AA subjects; however, potential regions of interest were identified. Established asthma SNPs were examined, seven from the NHGRI-EBI database and five with genome-wide significance in the largest pediatric asthma GWAS. Associations were found in the current childhood asthma GWAS with known asthma loci in IL1RL1, IL13, LINC01149, near GSDMB, and in the C11orf30-LRRC32 region (Bonferroni adjusted p < 0.05 for all comparisons). CONCLUSIONS: Childhood asthmatics are at increased risk for COPD. Defining asthma by self-report is valid in populations at risk for COPD, identifying subjects with clinical and genetic characteristics known to associate with childhood asthma. This has potential to improve clinical understanding of asthma-COPD overlap (ACO) and enhance future research into ACO-specific treatment regimens. TRIAL REGISTRATION: ClinicalTrials.gov, NCT00608764 (Active since January 28, 2008).
Mattsson N, Eriksson O, Lindberg O, Schöll M, Lampinen B, Nilsson M, Insel PS, Lautner R, Strandberg O, van Westen D, et al. Effects of APOE ε4 on neuroimaging, cerebrospinal fluid biomarkers, and cognition in prodromal Alzheimer's disease. Neurobiol Aging. 2018;71 :81-90.Abstract
Apolipoprotein (APOE) ε4 is a major genetic risk factor for Alzheimer's disease (AD), but its importance for the clinical and biological heterogeneity in AD is unclear, particularly at the prodromal stage. We analyzed 151 prodromal AD patients (44 APOE ε4-negative and 107 APOE ε4-positive) from the BioFINDER study. We tested cognition, 18F-flutemetamol β-amyloid (Aβ) positron emission tomography, cerebrospinal fluid biomarkers of Aβ, tau and neurodegeneration, and magnetic resonance imaging of white matter pathology and brain structure. Despite having similar cortical Aβ-load and baseline global cognition (mini mental state examination), APOE ε4-negative prodromal AD had more nonamnestic cognitive impairment, higher cerebrospinal fluid levels of Aβ-peptides and neuronal injury biomarkers, more white matter pathology, more cortical atrophy, and faster decline of mini mental state examination, compared to APOE ε4-positive prodromal AD. The absence of APOE ε4 is associated with an atypical phenotype of prodromal AD. This suggests that APOE ε4 may impact both the diagnostics of AD in early stages and potentially also effects of disease-modifying treatments.
Koppelmans V, Scott JM, Downs ME, Cassady KE, Yuan P, Pasternak O, Wood SJ, De Dios YE, Gadd NE, Kofman I, et al. Exercise effects on bed rest-induced brain changes. PLoS One. 2018;13 (10) :e0205515.Abstract
PURPOSE: Spaceflight negatively affects sensorimotor behavior; exercise mitigates some of these effects. Head down tilt bed rest (HDBR) induces body unloading and fluid shifts, and is often used to investigate spaceflight effects. Here, we examined whether exercise mitigates effects of 70 days HDBR on the brain and if fitness and brain changes with HDBR are related. METHODS: HDBR subjects were randomized to no-exercise (n = 5) or traditional aerobic and resistance exercise (n = 5). Additionally, a flywheel exercise group was included (n = 8). Exercise protocols for exercise groups were similar in intensity, therefore these groups were pooled in statistical analyses. Pre and post-HDBR MRI (structure and structural/functional connectivity) and physical fitness measures (lower body strength, muscle cross sectional area, VO2 max, body composition) were collected. Voxel-wise permutation analyses were used to test group differences in brain changes, and their associations with fitness changes. RESULTS: Comparisons of exercisers to controls revealed that exercise led to smaller fitness deterioration with HDBR but did not affect brain volume or connectivity. Group comparisons showed that exercise modulated post-HDBR recovery of brain connectivity in somatosensory regions. Posthoc analysis showed that this was related to functional connectivity decrease with HDBR in non-exercisers but not in exercisers. Correlational analyses between fitness and brain changes showed that fitness decreases were associated with functional connectivity and volumetric increases (all r >.74), potentially reflecting compensation. Modest brain changes or even decreases in connectivity and volume were observed in subjects who maintained or showed small fitness gains. These results did not survive Bonferroni correction, but can be considered meaningful because of the large effect sizes. CONCLUSION: Exercise performed during HDBR mitigates declines in fitness and strength. Associations between fitness and brain connectivity and volume changes, although unadjusted for multiple comparisons in this small sample, suggest that supine exercise reduces compensatory HDBR-induced brain changes.
Nilsson M, Englund E, Szczepankiewicz F, van Westen D, Sundgren PC. Imaging brain tumour microstructure. Neuroimage. 2018;182 :232-250.Abstract
Imaging is an indispensable tool for brain tumour diagnosis, surgical planning, and follow-up. Definite diagnosis, however, often demands histopathological analysis of microscopic features of tissue samples, which have to be obtained by invasive means. A non-invasive alternative may be to probe corresponding microscopic tissue characteristics by MRI, or so called 'microstructure imaging'. The promise of microstructure imaging is one of 'virtual biopsy' with the goal to offset the need for invasive procedures in favour of imaging that can guide pre-surgical planning and can be repeated longitudinally to monitor and predict treatment response. The exploration of such methods is motivated by the striking link between parameters from MRI and tumour histology, for example the correlation between the apparent diffusion coefficient and cellularity. Recent microstructure imaging techniques probe even more subtle and specific features, providing parameters associated to cell shape, size, permeability, and volume distributions. However, the range of scenarios in which these techniques provide reliable imaging biomarkers that can be used to test medical hypotheses or support clinical decisions is yet unknown. Accurate microstructure imaging may moreover require acquisitions that go beyond conventional data acquisition strategies. This review covers a wide range of candidate microstructure imaging methods based on diffusion MRI and relaxometry, and explores advantages, challenges, and potential pitfalls in brain tumour microstructure imaging.
Moutal N, Nilsson M, Topgaard D, Grebenkov D. The Kärger vs bi-exponential model: Theoretical insights and experimental validations. J Magn Reson. 2018;296 :72-78.Abstract
We revise three common models accounting for water exchange in pulsed-gradient spin-echo measurements: a bi-exponential model with time-dependent water fractions, the Kärger model, and a modified Kärger model designed for restricted diffusion, e.g. inside cells. The three models are compared and applied to experimental data from yeast cell suspensions. The Kärger model and the modified Kärger model yield very close results and accurately fit the data. The bi-exponential model, although less rigorous, has a natural physical interpretation and suggests a new experimental modality to estimate the water exchange time.
Panchal H, Sollmann N, Pasternak O, Alosco ML, Kinzel P, Kaufmann D, Hartl E, Forwell LA, Johnson AM, Skopelja EN, et al. Neuro-Metabolite Changes in a Single Season of University Ice Hockey Using Magnetic Resonance Spectroscopy. Front Neurol. 2018;9 :616.Abstract
Previous research has shown evidence for transient neuronal loss after repetitive head impacts (RHI) as demonstrated by a decrease in -acetylaspartate (NAA). However, few studies have investigated other neuro-metabolites that may be altered in the presence of RHI; furthermore, the relationship of neuro-metabolite changes to neurocognitive outcome and potential sex differences remain largely unknown. The aim of this study was to identify alterations in brain metabolites and their potential association with neurocognitive performance over time as well as to characterize sex-specific differences in response to RHI. 33 collegiate ice hockey players (17 males and 16 females) underwent 3T magnetic resonance spectroscopy (MRS) and neurocognitive evaluation before and after the Canadian Interuniversity Sports (CIS) ice hockey season 2011-2012. The MRS voxel was placed in the corpus callosum. Pre- and postseason neurocognitive performances were assessed using the Immediate Post-Concussion Assessment and Cognitive Test (ImPACT). Absolute neuro-metabolite concentrations were then compared between pre- and postseason MRS were (level of statistical significance after correction for multiple comparisons: < 0.007) and correlated to ImPACT scores for both sexes. A significant decrease in NAA was observed from preseason to postseason ( = 0.001). Furthermore, a trend toward a decrease in total choline (Cho) was observed ( = 0.044). Although no overall effect was observed for glutamate (Glu) over the season, a difference was observed with females showing a decrease in Glu and males showing an increase in Glu, though this was not statistically significant ( = 0.039). In both males and females, a negative correlation was observed between changes in Glu and changes in verbal memory ( = 0.008). The results of this study demonstrate changes in absolute concentrations of neuro-metabolites following exposure to RHI. Results suggest that changes in Glu are correlated with changes in verbal memory. Future studies need to investigate further the association between brain metabolites and clinical outcome as well as sex-specific differences in the brain's response to RHI.
Ramos-Llorden G, Vegas-Sanchez-Ferrero G, Bjork M, Vanhevel F, Parizel PM, Estepar RSJ, den Dekker AJ, Sijbers J. NOVIFAST: A Fast Algorithm for Accurate and Precise VFA MRI Mapping. IEEE Trans Med Imaging. 2018;37 (11) :2414-2427.Abstract
In quantitative magnetic resonance mapping, the variable flip angle (VFA) steady state spoiled gradient recalled echo (SPGR) imaging technique is popular as it provides a series of high resolution weighted images in a clinically feasible time. Fast, linear methods that estimate maps from these weighted images have been proposed, such as DESPOT1 and iterative re-weighted linear least squares. More accurate, non-linear least squares (NLLS) estimators are in play, but these are generally much slower and require careful initialization. In this paper, we present NOVIFAST, a novel NLLS-based algorithm specifically tailored to VFA SPGR mapping. By exploiting the particular structure of the SPGR model, a computationally efficient, yet accurate and precise map estimator is derived. Simulation and in vivo human brain experiments demonstrate a twenty-fold speed gain of NOVIFAST compared with conventional gradient-based NLLS estimators while maintaining a high precision and accuracy. Moreover, NOVIFAST is eight times faster than the efficient implementations of the variable projection (VARPRO) method. Furthermore, NOVIFAST is shown to be robust against initialization.
Simmross-Wattenberg F, Rodriguez-Cayetano M, Royuela-Del-Val J, Martin-Gonzalez E, Moya-Saez E, Martin-Fernandez M, Alberola-Lopez C. OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image Processing and Reconstruction on Heterogeneous Devices. IEEE J Biomed Health Inform. 2018.Abstract
Medical image processing is often limited by the computational cost of the involved algorithms. Whereas dedicated computing devices (GPUs in particular) exist and do provide significant efficiency boosts, they have an extra cost of use in terms of housekeeping tasks (device selection and initialization, data streaming, synchronization with the CPU and others), which may hinder developers from using them. This paper describes an OpenCL-based framework that is capable of handling dedicated computing devices seamlessly and that allows the developer to concentrate on image processing tasks. The framework handles automatically device discovery and initialization, data transfers to and from the device and the file system and kernel loading and compiling. Data structures need to be defined only once independently of the computing device; code is unique, consequently, for every device, including the host CPU. Pinned memory/buffer mapping is used to achieve maximum performance in data transfers. Code fragments included in the paper show how the computing device is almost immediately and effortlessly available to the users algorithms, so they can focus on productive work. Code required for device selection and initialization, data loading and streaming and kernel compilation is minimal and systematic. Algorithms can be thought of as mathematical operators (called processes), with input, output and parameters, and they may be chained one after another easily and efficiently. Also for efficiency, processes can have their initialization work split from their core workload, so process chains and loops do not incur in performance penalties. Algorithm code is independent of the device type targeted.
Nardelli P, Jimenez-Carretero D, Bermejo-Pelaez D, Washko GR, Rahaghi FN, Ledesma-Carbayo MJ, Estepar RSJ. Pulmonary Artery-Vein Classification in CT Images Using Deep Learning. IEEE Trans Med Imaging. 2018;37 (11) :2428-2440.Abstract
Recent studies show that pulmonary vascular diseases may specifically affect arteries or veins through different physiologic mechanisms. To detect changes in the two vascular trees, physicians manually analyze the chest computed tomography (CT) image of the patients in search of abnormalities. This process is time consuming, difficult to standardize, and thus not feasible for large clinical studies or useful in real-world clinical decision making. Therefore, automatic separation of arteries and veins in CT images is becoming of great interest, as it may help physicians to accurately diagnose pathological conditions. In this paper, we present a novel, fully automatic approach to classify vessels from chest CT images into arteries and veins. The algorithm follows three main steps: first, a scale-space particles segmentation to isolate vessels; then a 3-D convolutional neural network (CNN) to obtain a first classification of vessels; finally, graph-cuts' optimization to refine the results. To justify the usage of the proposed CNN architecture, we compared different 2-D and 3-D CNNs that may use local information from bronchus- and vessel-enhanced images provided to the network with different strategies. We also compared the proposed CNN approach with a random forests (RFs) classifier. The methodology was trained and evaluated on the superior and inferior lobes of the right lung of 18 clinical cases with noncontrast chest CT scans, in comparison with manual classification. The proposed algorithm achieves an overall accuracy of 94%, which is higher than the accuracy obtained using other CNN architectures and RF. Our method was also validated with contrast-enhanced CT scans of patients with chronic thromboembolic pulmonary hypertension to demonstrate that our model generalizes well to contrast-enhanced modalities. The proposed method outperforms state-of-the-art methods, paving the way for future use of 3-D CNN for artery/vein classification in CT images.
Chad JA, Pasternak O, Salat DH, Chen JJ. Re-examining age-related differences in white matter microstructure with free-water corrected diffusion tensor imaging. Neurobiol Aging. 2018;71 :161-170.Abstract
Diffusion tensor imaging (DTI) has been used extensively to investigate white matter (WM) microstructural changes during healthy adult aging. However, WM fibers are known to shrink throughout the lifespan, leading to larger interstitial spaces with age. This could allow more extracellular free water molecules to bias DTI metrics, which are relied upon to provide WM microstructural information. Using a cohort of 212 participants, we demonstrate that WM microstructural changes in aging are potentially less pronounced than previously reported once the free water compartment is eliminated. After free water elimination, DTI parameters show age-related differences that match histological evidence of myelin degradation and debris accumulation. The fraction of free water is further shown to associate better with age than any of the conventional DTI parameters. Our findings suggest that DTI analyses involving free water are likely to yield novel insight into retrospective re-analysis of data and to answer new questions in ongoing DTI studies of brain aging.

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