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Thijs Dhollander

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22 papers

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YNICL Journal 2024 Journal Article

Associations between low-moderate prenatal alcohol exposure and brain development in childhood

Deanne K. Thompson
Claire E. Kelly
Thijs Dhollander
Evelyne Muggli
Stephen Hearps
Sharon Lewis
Thi-Nhu-Ngoc Nguyen
Alicia Spittle

BACKGROUND: The effects of low-moderate prenatal alcohol exposure (PAE) on brain development have been infrequently studied. AIM: To compare cortical and white matter structure between children aged 6 to 8 years with low-moderate PAE in trimester 1 only, low-moderate PAE throughout gestation, or no PAE. METHODS: -weighted images were processed using FreeSurfer, obtaining brain volume, area, and thickness of 34 cortical regions per hemisphere. Fibre density (FD), fibre cross-section (FC) and fibre density and cross-section (FDC) metrics were computed for diffusion images. Brain measures were compared between PAE groups adjusted for age and sex, then additionally for intracranial volume. RESULTS: < 0.05) were smaller in children exposed to alcohol throughout gestation compared with no PAE. CONCLUSION: This study reports a relationship between low-moderate PAE throughout gestation and cingulate cortex and cingulum tract alterations, suggesting a teratogenic vulnerability. Further investigation is warranted.

YNICL Journal 2024 Journal Article

Structural brain network organization in children with prenatal alcohol exposure

Xiaoyun Liang
Claire E. Kelly
Chun-Hung Yeh
Thijs Dhollander
Stephen Hearps
Peter J. Anderson
Deanne K. Thompson

INTRODUCTION: There is growing evidence suggesting that children with prenatal alcohol exposure (PAE) struggle with cognitively demanding tasks, such as learning, attention, and language. Complex structural network analyses can provide insight into the neurobiological underpinnings of these functions, as they may be sensitive for characterizing the effects of PAE on the brain. However, investigations on how PAE affects brain networks are limited. We aim to compare diffusion magnetic resonance imaging (MRI) tractography-based structural networks between children with low-to-moderate PAE in trimester 1 only (T1) or throughout all trimesters (T1-T3) with those without alcohol exposure prenatally. METHODS: Our cohort included three groups of children aged 6 to 8 years: 1) no PAE (n = 24), 2) low-to-moderate PAE during T1 only (n = 30), 3) low-to-moderate PAE throughout T1-T3 (n = 36). Structural networks were constructed using the multi-shell multi-tissue constrained spherical deconvolution tractography technique. Quantitative group-wise analyses were conducted at three levels: (a) at the whole-brain network level, using both network-based statistical analyses and network centrality; and then using network centrality at (b) the modular level, and (c) per-region level, including the regions identified as brain hubs. RESULTS: Compared with the no PAE group, widespread brain network alterations were observed in the PAE T1-T3 group using network-based statistics, but no alterations were observed for the PAE T1 group. Network alterations were also detected at the module level in the PAE T1-T3 compared with the no PAE group, with lower eigenvector centrality in the module that closely represented the right cortico-basal ganglia-thalamo-cortical network. No significant group differences were found in network centrality at the per-region level, including the hub regions. CONCLUSIONS: This study demonstrated that low-to-moderate PAE throughout pregnancy may alter brain structural connectivity, which may explain the neurodevelopmental deficits associated with PAE. It is possible that timing and duration of alcohol exposure are crucial, as PAE in T1 only did not appear to alter brain structural connectivity.

YNIMG Journal 2022 Journal Article

Brain tissue microstructural and free-water composition 13 years after very preterm birth

Claire Kelly
Thijs Dhollander
Ian H Harding
Wasim Khan
Richard Beare
Jeanie LY Cheong
Lex W Doyle
Marc Seal

There have been many studies demonstrating children born very preterm exhibit brain white matter microstructural alterations, which have been related to neurodevelopmental difficulties. These prior studies have often been based on diffusion MRI modelling and analysis techniques, which commonly focussed on white matter microstructural properties in children born very preterm. However, there have been relatively fewer studies investigating the free-water content of the white matter, and also the microstructure and free-water content of the cortical grey matter, in children born very preterm. These biophysical properties of the brain change rapidly during fetal and neonatal brain development, and therefore such properties are likely also adversely affected by very preterm birth. In this study, we investigated the relationship of very preterm birth (<30 weeks' gestation) to both white matter and cortical grey matter microstructure and free-water content in childhood using advanced diffusion MRI analyses. A total of 130 very preterm participants and 45 full-term control participants underwent diffusion MRI at age 13 years. Diffusion tissue signal fractions derived by Single-Shell 3-Tissue Constrained Spherical Deconvolution were used to investigate brain tissue microstructural and free-water composition. The tissue microstructural and free-water composition metrics were analysed using a voxel-based analysis and cortical region-of-interest analysis approach. Very preterm 13-year-olds exhibited reduced white matter microstructural density and increased free-water content across widespread regions of the white matter compared with controls. Additionally, very preterm 13-year-olds exhibited reduced microstructural density and increased free-water content in specific temporal, frontal, occipital and cingulate cortical regions. These brain tissue composition alterations were strongly associated with cerebral white matter abnormalities identified in the neonatal period, and concurrent adverse cognitive and motor outcomes in very preterm children. The findings demonstrate brain microstructural and free-water alterations up to thirteen years from neonatal brain abnormalities in very preterm children that relate to adverse neurodevelopmental outcomes.

YNICL Journal 2022 Journal Article

Structural brain connectivity in children after neonatal stroke: A whole-brain fixel-based analysis

Pablo Pretzel
Thijs Dhollander
Stéphane Chabrier
Mariam Al-Harrach
Lucie Hertz-Pannier
Mickael Dinomais
Samuel Groeschel

INTRODUCTION: Neonatal arterial ischemic stroke (NAIS) has been shown to affect white matter (WM) microstructure beyond the lesion. Here, we employed fixel-based analysis, a technique which allows to model and interpret WM alterations in complex arrangements such as crossing fibers, to further characterize the long-term effects of NAIS on the entire WM outside the primary infarct area. MATERIALS AND METHODS: 32 children (mean age 7.3 years (SD 0.4), 19 male) with middle cerebral artery NAIS (18 left hemisphere, 14 right hemisphere) and 31 healthy controls (mean age 7.7 years (SD 0.6), 16 male) underwent diffusion MRI scans and clinical examination for manual dexterity. Microstructural and macrostructural properties of the WM were investigated in a fixel-based whole-brain analysis, which allows to detect fiber-specific effects. Additionally, tract-averaged fixel metrics in interhemispheric tracts, and their correlation with manual dexterity, were examined. RESULTS: Significantly reduced microstructural properties were identified, located within the parietal and temporal WM of the affected hemisphere, as well as within their interhemispheric connecting tracts. Tract-averaged fixel metrics showed moderate, significant correlation with manual dexterity of the affected hand. No increased fixel metrics or contralesional alterations were observed. DISCUSSION: Our results show that NAIS leads to long-term alterations in WM microstructure distant from the lesion site, both within the parietal and temporal lobes as well as in their interhemispheric connections. The functional significance of these findings is demonstrated by the correlations with manual dexterity. The localization of alterations in structures highly connected to the lesioned areas shift our perception of NAIS from a focal towards a developmental network injury.

YNICL Journal 2022 Journal Article

Timing of selective basal ganglia white matter loss in premanifest Huntington’s disease

Paul Zeun
Peter McColgan
Thijs Dhollander
Sarah Gregory
Eileanoir B. Johnson
Marina Papoutsi
Akshay Nair
Rachael I. Scahill

OBJECTIVES: To investigate the timeframe prior to symptom onset when cortico-basal ganglia white matter (white matter) loss begins in premanifest Huntington's disease (preHD), and which striatal and thalamic sub-region white matter tracts are most vulnerable. METHODS: We performed fixel-based analysis, which allows resolution of crossing white matter fibres at the voxel level, on diffusion tractography derived white matter tracts of striatal and thalamic sub-regions in two independent cohorts; TrackON-HD, which included 72 preHD (approx. 11 years before disease onset) and 85 controls imaged at three time points over two years; and the HD young adult study (HD-YAS), which included 54 preHD (approx. 25 years before disease onset) and 53 controls, imaged at one time point. Group differences in fibre density and cross section (FDC) were investigated. RESULTS: We found no significant group differences in cortico-basal ganglia sub-region FDC in preHD gene carriers 25 years before onset. In gene carriers 11 years before onset, there were reductions in striatal (limbic and caudal motor) and thalamic (premotor, motor and sensory) FDC at baseline, with no significant change over 2 years. Caudal motor-striatal, pre-motor-thalamic, and primary motor-thalamic FDC at baseline, showed significant correlations with the Unified Huntington's disease rating scale (UHDRS) total motor score (TMS). Limbic cortico-striatal FDC and apathy were also significantly correlated. CONCLUSIONS: Our findings suggest that limbic and motor white matter tracts to the striatum and thalamus are most susceptible to early degeneration in HD but that approximately 25 years from onset, these tracts appear preserved. These findings may have importance in determining the optimum time to initiate future disease modifying therapies in HD.

YNIMG Journal 2021 Journal Article

Fibre-specific laterality of white matter in left and right language dominant people

Helena Verhelst
Thijs Dhollander
Robin Gerrits
Guy Vingerhoets

Language is the most commonly described lateralised cognitive function, relying more on the left hemisphere compared to the right hemisphere in over 90% of the population. Most research examining the structure-function relationship of language lateralisation only included people showing a left language hemisphere dominance. In this work, we applied a state-of-the-art "fixel-based" analysis approach, allowing statistical analysis of white matter micro- and macrostructure on a fibre-specific level in a sample of participants with left and right language dominance (LLD and RLD). Both groups showed a similar extensive pattern of white matter lateralisation including a comparable leftwards lateralisation of the arcuate fasciculus, regardless of their functional language lateralisation. These results suggest that lateralisation of language functioning and the arcuate fasciculus are driven by independent biases. Finally, a significant group difference of lateralisation was detected in the forceps minor, with a leftwards lateralisation in LLD and rightwards lateralisation for the RLD group.

YNIMG Journal 2021 Journal Article

Fixel-based Analysis of Diffusion MRI: Methods, Applications, Challenges and Opportunities

Thijs Dhollander
Adam Clemente
Mervyn Singh
Frederique Boonstra
Oren Civier
Juan Dominguez Duque
Natalia Egorova
Peter Enticott

Diffusion MRI has provided the neuroimaging community with a powerful tool to acquire in-vivo data sensitive to microstructural features of white matter, up to 3 orders of magnitude smaller than typical voxel sizes. The key to extracting such valuable information lies in complex modelling techniques, which form the link between the rich diffusion MRI data and various metrics related to the microstructural organization. Over time, increasingly advanced techniques have been developed, up to the point where some diffusion MRI models can now provide access to properties specific to individual fibre populations in each voxel in the presence of multiple "crossing" fibre pathways. While highly valuable, such fibre-specific information poses unique challenges for typical image processing pipelines and statistical analysis. In this work, we review the "Fixel-Based Analysis" (FBA) framework, which implements bespoke solutions to this end. It has recently seen a stark increase in adoption for studies of both typical (healthy) populations as well as a wide range of clinical populations. We describe the main concepts related to Fixel-Based Analyses, as well as the methods and specific steps involved in a state-of-the-art FBA pipeline, with a focus on providing researchers with practical advice on how to interpret results. We also include an overview of the scope of all current FBA studies, categorized across a broad range of neuro-scientific domains, listing key design choices and summarizing their main results and conclusions. Finally, we critically discuss several aspects and challenges involved with the FBA framework, and outline some directions and future opportunities.

YNIMG Journal 2021 Journal Article

Investigating the microstructural properties of normal-appearing white matter (NAWM) preceding conversion to white matter hyperintensities (WMHs) in stroke survivors

Wasim Khan
Mohamed Salah Khlif
Remika Mito
Thijs Dhollander
Amy Brodtmann

Using advanced diffusion MRI, we aimed to assess the microstructural properties of normal-appearing white matter (NAWM) preceding conversion to white matter hyperintensities (WMHs) using 3-tissue diffusion signal compositions in ischemic stroke. Data were obtained from the Cognition and Neocortical Volume After Stroke (CANVAS) study. Diffusion-weighted MR and high-resolution structural brain images were acquired 3- (baseline) and 12-months (follow-up) post-stroke. WMHs were automatically segmented and longitudinal assessment at 12-months was used to retrospectively delineate NAWM voxels at baseline converting to WMHs. NAWM voxels converting to WMHs were further dichotomized into either: “growing” WMHs if NAWM adhered to existing WMH voxels, or “isolated de-novo" WMHs if NAWM was unconnected to WMH voxels identified at baseline. Microstructural properties were assessed using 3-tissue diffusion signal compositions consisting of white matter-like (WM-like: TW), gray matter-like (GM-like: TG), and cerebrospinal fluid-like (CSF-like: TC) signal fractions. Our findings showed that NAWM converting to WMHs already exhibited similar changes in tissue compositions at baseline to WMHs with lower TW and increased TC (fluid-like, i. e. free-water) and TG compared to persistent NAWM. We also found that microstructural properties of persistent NAWM were related to overall WMH burden with greater free-water content in patients with high WMH load. These findings suggest that NAWM preceding conversion to WMHs are accompanied by greater fluid-like properties indicating increased tissue water content. Increased GM-like properties may indicate a more isotropic microstructure of tissue reflecting a degree of hindered diffusion in NAWM regions vulnerable to WMH development. These results support the usefulness of microstructural compositions as a sensitive marker of NAWM vulnerability to WMH pathogenesis.

YNIMG Journal 2020 Journal Article

Early childhood development of white matter fiber density and morphology

Dennis Dimond
Christiane S. Rohr
Robert E. Smith
Thijs Dhollander
Ivy Cho
Catherine Lebel
Deborah Dewey
Alan Connelly

Early childhood is an important period for cognitive and brain development, though white matter changes specific to this period remain understudied. Here we utilize a novel analytic approach to quantify and track developmental changes in white matter micro- and macro-structure, calculated from individually oriented fiber-bundle populations, termed “fixels”. Fixel-based analysis and mixed-effects models were used to assess tract-wise changes in fiber density and bundle morphology in 73 girls scanned at baseline (ages 4. 09–7. 02, mean = 5. 47, SD = 0. 81), 6-month (N = 7), and one-year follow-up (N = 42). For comparison, we also assessed changes in commonly utilized diffusion tensor metrics: fractional anisotropy (FA), and mean, radial and axial diffusivity (MD, RD, AD). Maturational increases in fixel-metrics were seen in most major white matter tracts, with the most rapid increases in the corticospinal tract and slowest or non-significant increases in the genu of the corpus callosum and uncinate fasciculi. As expected, we observed developmental increases in FA and decreases in MD, RD and AD, though percent changes were smaller relative to fixel-metrics. The majority of tracts showed more substantial morphological than microstructural changes. These findings highlight early childhood as a period of dynamic white matter maturation, characterized by large increases in macroscopic fiber bundle size, mild changes in axonal density, and parallel, albeit less substantial, changes in diffusion tensor metrics.

YNIMG Journal 2020 Journal Article

Fiber-specific variations in anterior transcallosal white matter structure contribute to age-related differences in motor performance

Hamed Zivari Adab
Sima Chalavi
Thiago S. Monteiro
Jolien Gooijers
Thijs Dhollander
Dante Mantini
Stephan P. Swinnen

Age-related differences in bimanual motor performance have been extensively documented, but their underlying neural mechanisms remain less clear. Studies applying diffusion MRI in the aging population have revealed evidence for age-related white matter variations in the corpus callosum (CC) which are related to bimanual motor performance. However, the diffusion tensor model used in those studies is confounded by partial volume effects in voxels with complex fiber geometries which are present in up to 90% of white matter voxels, including the bilateral projections of the CC. A recently developed whole-brain analysis framework, known as fixel-based analysis (FBA), enables comprehensive statistical analyses of white matter quantitative measures in the presence of such complex fiber geometries. To investigate the contribution of age-related fiber-specific white matter variations to age-related differences in bimanual performance, a cross-sectional lifespan sample of healthy human adults (N = 95; 20–75 years of age) performed a bimanual tracking task. Furthermore, diffusion MRI data were acquired and the FBA metrics associated with fiber density, cross-section, and combined fiber density and cross-section were estimated. Whole-brain FBA revealed significant negative associations between age and fiber density, cross-section, and combined metrics of multiple white matter tracts, including the bilateral projections of the CC, indicative of white matter micro- and macrostructural degradation with age. More importantly, mediation analyses demonstrated that age-related variations in the combined (fiber density and cross-section) metric of the genu, but not splenium, of the CC contributed to the observed age-related differences in bimanual coordination performance. These findings highlight the contribution of variations in interhemispheric communication between prefrontal (non-motor) cortices to age-related differences in motor performance.

YNICL Journal 2020 Journal Article

In vivo microstructural heterogeneity of white matter lesions in healthy elderly and Alzheimer's disease participants using tissue compositional analysis of diffusion MRI data

Remika Mito
Thijs Dhollander
Ying Xia
David Raffelt
Olivier Salvado
Leonid Churilov
Christopher C. Rowe
Amy Brodtmann

White matter hyperintensities (WMH) are regions of high signal intensity typically identified on fluid attenuated inversion recovery (FLAIR). Although commonly observed in elderly individuals, they are more prevalent in Alzheimer's disease (AD) patients. Given that WMH appear relatively homogeneous on FLAIR, they are commonly partitioned into location- or distance-based classes when investigating their relevance to disease. Since pathology indicates that such lesions are often heterogeneous, probing their microstructure in vivo may provide greater insight than relying on such arbitrary classification schemes. In this study, we investigated WMH in vivo using an advanced diffusion MRI method known as single-shell 3-tissue constrained spherical deconvolution (SS3T-CSD), which models white matter microstructure while accounting for grey matter and CSF compartments. Diffusion MRI data and FLAIR images were obtained from AD (n = 48) and healthy elderly control (n = 94) subjects. WMH were automatically segmented, and classified: (1) as either periventricular or deep; or (2) into three distance-based contours from the ventricles. The 3-tissue profile of WMH enabled their characterisation in terms of white matter-, grey matter-, and fluid-like characteristics of the diffusion signal. Our SS3T-CSD findings revealed substantial heterogeneity in the 3-tissue profile of WMH, both within lesions and across the various classes. Moreover, this heterogeneity information indicated that the use of different commonly used WMH classification schemes can result in different disease-based conclusions. We conclude that future studies of WMH in AD would benefit from inclusion of microstructural information when characterising lesions, which we demonstrate can be performed in vivo using SS3T-CSD.

YNIMG Journal 2020 Journal Article

Maturation and interhemispheric asymmetry in neurite density and orientation dispersion in early childhood

Dennis Dimond
Stella Heo
Amanda Ip
Christiane S. Rohr
Ryann Tansey
Kirk Graff
Thijs Dhollander
Robert E. Smith

Background The brain's white matter undergoes profound changes during early childhood, which are believed to underlie the rapid development of cognitive and behavioral skills during this period. Neurite density, and complexity of axonal projections, have been shown to change across the life span, though changes during early childhood are poorly characterized. Here, we utilize neurite orientation dispersion and density imaging (NODDI) to investigate maturational changes in tract-wise neurite density index (NDI) and orientation dispersion index (ODI) during early childhood. Additionally, we assess hemispheric asymmetry of tract-wise NDI and ODI values, and longitudinal changes. Methods Two sets of diffusion weighted images with different diffusion-weighting were collected from 125 typically developing children scanned at baseline (N = 125; age range = 4. 14–7. 29; F/M = 73/52), 6-month (N = 8; F/M = 8/0), and 12-month (N = 52; F/M = 39/13) timepoints. NODDI and template-based tractography using constrained spherical deconvolution were utilized to calculate NDI and ODI values for major white matter tracts. Mixed-effects models controlling for sex, handedness, and in-scanner head motion were utilized to assess developmental changes in tract-wise NDI and ODI. Additional mixed-effects models were used to assess interhemispheric differences in tract-wise NDI and ODI values and hemispheric asymmetries in tract-wise development. Results Maturational increases in NDI were seen in all major white matter tracts, though we did not observe the expected tract-wise pattern of maturational rates (e. g. fast commissural/projection and slow frontal/temporal tract change). ODI did not change significantly with age in any tract. We observed greater NDI and ODI values in the right as compared to the left hemisphere for most tracts, but no hemispheric asymmetry for rate of change with age. Conclusions These findings suggest that neurite density, but not orientation dispersion, increases with age during early childhood. In relation to NDI growth trends reported in infancy and late-childhood, our results suggest that early childhood may be a transitional period for neurite density maturation wherein commissural/projection fibers are approaching maturity, maturation in long range association fibers is increasing, and changes in limbic/frontal fibers remain modest. Rightward asymmetry in NDI and ODI values, but no asymmetry in developmental changes, suggests that rightward asymmetry of neurite density and orientation dispersion is established prior to age 4.

YNIMG Journal 2020 Journal Article

Modeling brain dynamics after tumor resection using The Virtual Brain

Hannelore Aerts
Michael Schirner
Thijs Dhollander
Ben Jeurissen
Eric Achten
Dirk Van Roost
Petra Ritter
Daniele Marinazzo

Brain tumor patients scheduled for tumor resection often face significant uncertainty, as the outcome of neurosurgery is difficult to predict at the individual patient level. Recently, simulation of the activity of neural populations connected according to the white matter fibers, producing personalized brain network models, has been introduced as a promising tool for this purpose. The Virtual Brain provides a robust open source framework to implement these models. However, brain network models first have to be validated, before they can be used to predict brain dynamics. In prior work, we optimized individual brain network model parameters to maximize the fit with empirical brain activity. In this study, we extend this line of research by examining the stability of fitted parameters before and after tumor resection, and compare it with baseline parameter variability using data from healthy control subjects. Based on these findings, we perform the first “virtual neurosurgery”, mimicking patient’s actual surgery by removing white matter fibers in the resection mask and simulating again neural activity on this new connectome. We find that brain network model parameters are relatively stable over time in brain tumor patients who underwent tumor resection, compared with baseline variability in healthy control subjects. Concerning the virtual neurosurgery analyses, use of the pre-surgery model implemented on the virtually resected structural connectome resulted in improved similarity with post-surgical empirical functional connectivity in some patients, but negligible improvement in others. These findings reveal interesting avenues for increasing interactions between computational neuroscience and neuro-oncology, as well as important limitations that warrant further investigation.

YNIMG Journal 2020 Journal Article

Three-tissue compositional analysis reveals in-vivo microstructural heterogeneity of white matter hyperintensities following stroke

Wasim Khan
Natalia Egorova
Mohamed Salah Khlif
Remika Mito
Thijs Dhollander
Amy Brodtmann

White matter hyperintensities (WMHs) are frequently observed on brain scans of older individuals and are associated with cognitive impairment and vascular brain burden. Recent studies have shown that WMHs may only represent an extreme end of a diffuse pathological spectrum of white matter (WM) degeneration. The present study investigated the microstructural characteristics of WMHs using an advanced diffusion MRI modelling approach known as Single-Shell 3-Tissue Constrained Spherical Deconvolution (SS3T-CSD), which provides information on different tissue compartments within each voxel. The SS3T-CSD method may provide complementary information in the interpretation of pathological tissue through the tissue-specific microstructural compositions of WMHs. Data were obtained from stroke patients enrolled in the Cognition and Neocortical Volume After Stroke (CANVAS) study, a study examining brain volume and cognition after stroke. WMHs were segmented using an automated method, based on fluid attenuated inversion recovery (FLAIR) images. Automated tissue segmentation was used to identify normal-appearing white matter (NAWM). WMHs were classified into juxtaventricular, periventricular and deep lesions, based on their distance from the ventricles (3–10 mm). We aimed to compare in stroke participants the microstructural composition of the different lesion classes of WMHs and compositions of NAWM to assess the in-vivo heterogeneity of these lesions. Results showed that the 3-tissue composition significantly differed between WMHs classes and NAWM. Specifically, the 3-tissue compositions for juxtaventricular and periventricular WMHs both exhibited a relatively greater fluid-like (free water) content, which is compatible with a presence of interstitial fluid accumulation, when compared to deep WMHs. These findings provide evidence of microstructural heterogeneity of WMHs in-vivo and may support new insights for understanding the role of WMH development in vascular neurodegeneration.

YNICL Journal 2019 Journal Article

Advanced MRI analysis to detect white matter brain injury in growth restricted newborn lambs

Atul Malhotra
Tara Sepehrizadeh
Thijs Dhollander
David Wright
Margie Castillo-Melendez
Amy E. Sutherland
Yen Pham
Michael Ditchfield

BACKGROUND: Fetal growth restriction (FGR) is a serious pregnancy complication associated with increased risk of adverse neurodevelopment and neuromorbidity. Current imaging techniques, including conventional magnetic resonance imaging (MRI), are not sensitive enough to detect subtle structural abnormalities in the FGR brain. We examined whether advanced MRI analysis techniques have the capacity to detect brain injury (particularly white matter injury) caused by chronic hypoxia-induced fetal growth restriction in newborn preterm lambs. METHODS: Surgery was undertaken in twin bearing pregnant ewes at 88-90 days gestation (term = 150 days) to induce FGR in one fetus. At 127 days gestation (~32 weeks human brain development), FGR and control (appropriate for gestational age, AGA) lambs were delivered by caesarean section, intubated and ventilated. Conventional and advanced brain imaging was conducted within the first two hours of life using a 3T MRI scanner. T1-weighted (T1w) and T2-weighted (T2w) structural imaging, magnetic resonance spectroscopy (MRS), and diffusion MRI (dMRI) data were acquired. Diffusion tensor imaging (DTI) modelling and analysis of dMRI data included the following regions of interest (ROIs): subcortical white matter, periventricular white matter, cerebellum, hippocampus, corpus callosum and thalamus. Fixel-based analysis of 3-tissue constrained spherical deconvolution (CSD) of the dMRI data was performed and compared between FGR and AGA lambs. Lambs were euthanised immediately after the scans and brain histology performed in the regions of interest to correlate with imaging. RESULTS: FGR and AGA lamb (body weight, mean (SD): 2.2(0.5) vs. 3.3(0.3) kg, p = .002) MRI brain scans were analysed. There were no statistically significant differences observed between the groups in conventional T1w, T2w or MRS brain data. Mean, axial and radial diffusivity, and fractional anisotropy indices obtained from DTI modelling also did not show any statistically significant differences between groups in the ROIs. Fixel-based analysis of 3-tissue CSD, however, did reveal a decrease in fibre cross-section (FC, p < .05) but not in fibre density (FD) or combined fibre density and cross-section (FDC) in FGR vs. AGA lamb brains. The specific tracts that showed a decrease in FC were in the regions of the periventricular white matter, hippocampus and cerebellar white matter, and were supported by histological evidence of white matter hypomyelination and disorganisation in corresponding FGR lamb brain regions. CONCLUSIONS: The neuropathology associated with FGR in neonatal preterm lambs is subtle and imaging detection may require advanced MRI and tract-based analysis techniques. Fixel-based analysis of 3-tissue CSD demonstrates that the preterm neonatal FGR brain shows evidence of macrostructural (cross-sectional) deficits in white matter subsequent to altered antenatal development. These findings can inform analysis of similar brain pathology in neonatal infants.

YNIMG Journal 2019 Journal Article

Connectomes from streamlines tractography: Assigning streamlines to brain parcellations is not trivial but highly consequential

Chun-Hung Yeh
Robert E. Smith
Thijs Dhollander
Fernando Calamante
Alan Connelly

When using diffusion MRI streamlines tractograms to construct structural connectomes, ideally, each streamline should connect exactly 2 regions-of-interest (i. e. network nodes) as defined by a given brain parcellation scheme. However, the ill-posed nature of termination criteria in many tractography algorithms can cause streamlines apparently being associated with zero, one, or more than two grey matter (GM) nodes; streamlines that terminate in white matter or cerebrospinal fluid may even end up being assigned to nodes if the definitions of these nodes are not strictly constrained to genuine GM areas, resulting in a misleading connectome in non-trivial ways. Based on both in-house MRI data and state-of-the-art data provided by the Human Connectome Project, this study investigates the actual influence of streamline-to-node assignment methods, and their interactions with fibre-tracking terminations and brain parcellations, on the construction of pairwise regional connectivity and subsequent connectomic measures. Our results show that the frequency of generating successful pairwise connectivity is heavily affected by the convoluted interactions between the applied strategies for connectome construction, and that minor changes in the mechanism can cause significant variations in the within- and between-module connectivity strengths as well as in the commonly-used graph theory metrics. Our data suggest that these fundamental processes should not be overlooked in structural connectomics research, and that improved data quality is not in itself sufficient to solve the underlying problems associated with assigning streamlines to brain nodes. We demonstrate that the application of advanced fibre-tracking techniques that are designed to correct for inaccuracies of track terminations with respect to anatomical information at the fibre-tracking stage is advantageous to the subsequent connectome construction process, in which pairs of parcellation nodes can be more robustly identified from streamline terminations via a suitable assignment mechanism.

YNIMG Journal 2019 Journal Article

MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

J-Donald Tournier
Robert Smith
David Raffelt
Rami Tabbara
Thijs Dhollander
Maximilian Pietsch
Daan Christiaens
Ben Jeurissen

MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software.

YNICL Journal 2018 Journal Article

Fibre-specific white matter changes in multiple sclerosis patients with optic neuritis

Sanuji Gajamange
David Raffelt
Thijs Dhollander
Elaine Lui
Anneke van der Walt
Trevor Kilpatrick
Joanne Fielding
Alan Connelly

Long term irreversible disability in multiple sclerosis (MS) is thought to be primarily driven by axonal degeneration. Axonal degeneration leads to degenerative atrophy, therefore early markers of axonal degeneration are required to predict clinical disability and treatment efficacy. Given that additional pathologies such as inflammation, demyelination and oedema are also present in MS, it is essential to develop axonal markers that are not confounded by these processes. The present study investigated a novel method for measuring axonal degeneration in MS based on high angular resolution diffusion magnetic resonance imaging. Unlike standard methods, this novel method involved advanced acquisition and modelling for improved axonal sensitivity and specificity. Recent work has developed analytical methods, two novel axonal markers, fibre density and cross-section, that can be estimated for each fibre direction in each voxel (termed a "fixel"). This technique, termed fixel-based analysis, thus simultaneously estimates axonal density and white matter atrophy from specific white matter tracts. Diffusion-weighted imaging datasets were acquired for 17 patients with a history of acute unilateral optic neuritis (35.3 ± 10.2 years, 11 females) and 14 healthy controls (32.7 ± 4.8 years, 8 females) on a 3 T scanner. Fibre density values were compared to standard diffusion tensor imaging parameters (fractional anisotropy and mean diffusivity) in lesions and normal appearing white matter. Group comparisons were performed for each fixel to assess putative differences in fibre density and fibre cross-section. Fibre density was observed to have a comparable sensitivity to fractional anisotropy for detecting white matter pathology in MS, but was not affected by crossing axonal fibres. Whole brain fixel-based analysis revealed significant reductions in fibre density and fibre cross-section in the inferior fronto-occipital fasciculus (including the optic radiations) of patients compared to controls. We interpret this result to indicate that this fixel-based approach is able to detect early loss of fibre density and cross-section in the optic radiations in MS patients with a history of optic neuritis. Fibre-specific markers of axonal degeneration should be investigated further for use in early stage therapeutic trials, or to monitor axonal injury in early stage MS.

YNIMG Journal 2017 Journal Article

White matter alterations at pubertal onset

Sila Genc
Marc L. Seal
Thijs Dhollander
Charles B. Malpas
Philip Hazell
Timothy J. Silk

Recent neurodevelopmental research supports the contribution of pubertal stage to local and global grey and white matter remodelling. Little is known, however, about white matter microstructural alterations at pubertal onset. This study investigated differences in white matter properties between pre-pubertal and pubertal children using whole brain fixel-based analysis (FBA) of the microscopic density and macroscopic cross-section of fibre bundles. Diffusion-weighted imaging data were acquired for 74 typically developing children (M=10. 4, SD=. 43 years, 31 female) at 3. 0T (60 diffusion gradient directions, b-value=2800s/mm2). Group comparisons of fibre density (FD) and fibre cross-section (FC) were made between age-matched pre-pubertal and pubertal groups, and post-hoc analyses were performed on regions of interest (ROIs) defined in the splenium, body and genu of the corpus callosum. Significant fixel-wise differences in FD were observed between the pubertal groups, where the pubertal group had significantly higher FD compared with age-matched pre-pubertal children, localised to the posterior corpus callosum. Post-hoc analyses on mean FD in the corpus callosum ROIs revealed group differences between the pubertal groups in the splenium, but not body or genu. The observed higher apparent fibre density in the splenium suggests that pubertal onset coincides with white matter differences explained by increasing axon diameter. This may be an important effect to account for over pubertal development, particularly for group studies where age-matched clinical and typical populations may be at various stages of puberty.

YNIMG Journal 2015 Journal Article

Global tractography of multi-shell diffusion-weighted imaging data using a multi-tissue model

Daan Christiaens
Marco Reisert
Thijs Dhollander
Stefan Sunaert
Paul Suetens
Frederik Maes

Diffusion-weighted imaging and tractography provide a unique, non-invasive technique to study the macroscopic structure and connectivity of brain white matter in vivo. Global tractography methods aim at reconstructing the full-brain fiber configuration that best explains the measured data, based on a generative signal model. In this work, we incorporate a multi-shell multi-tissue model based on spherical convolution, into a global tractography framework, which allows to deal with partial volume effects. The required tissue response functions can be estimated from and hence calibrated to the data. The resulting track reconstruction is quantitatively related to the apparent fiber density in the data. In addition, the fiber orientation distribution for white matter and the volume fractions of gray matter and cerebrospinal fluid are produced as ancillary results. Validation results on simulated data demonstrate that this data-driven approach improves over state-of-the-art streamline and global tracking methods, particularly in the valid connection rate. Results in human brain data correspond to known white matter anatomy and show improved modeling of partial voluming. This work is an important step toward detecting and quantifying white matter changes and connectivity in healthy subjects and patients.

YNIMG Journal 2014 Journal Article

Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data

Ben Jeurissen
Jacques-Donald Tournier
Thijs Dhollander
Alan Connelly
Jan Sijbers

Constrained spherical deconvolution (CSD) has become one of the most widely used methods to extract white matter (WM) fibre orientation information from diffusion-weighted MRI (DW-MRI) data, overcoming the crossing fibre limitations inherent in the diffusion tensor model. It is routinely used to obtain high quality fibre orientation distribution function (fODF) estimates and fibre tractograms and is increasingly used to obtain apparent fibre density (AFD) measures. Unfortunately, CSD typically only supports data acquired on a single shell in q-space. With multi-shell data becoming more and more prevalent, there is a growing need for CSD to fully support such data. Furthermore, CSD can only provide high quality fODF estimates in voxels containing WM only. In voxels containing other tissue types such as grey matter (GM) and cerebrospinal fluid (CSF), the WM response function may no longer be appropriate and spherical deconvolution produces unreliable, noisy fODF estimates. The aim of this study is to incorporate support for multi-shell data into the CSD approach as well as to exploit the unique b-value dependencies of the different tissue types to estimate a multi-tissue ODF. The resulting approach is dubbed multi-shell, multi-tissue CSD (MSMT-CSD) and is compared to the state-of-the-art single-shell, single-tissue CSD (SSST-CSD) approach. Using both simulations and real data, we show that MSMT-CSD can produce reliable WM/GM/CSF volume fraction maps, directly from the DW data, whereas SSST-CSD has a tendency to overestimate the WM volume in voxels containing GM and/or CSF. In addition, compared to SSST-CSD, MSMT-CSD can substantially increase the precision of the fODF fibre orientations and reduce the presence of spurious fODF peaks in voxels containing GM and/or CSF. Both effects translate into more reliable AFD measures and tractography results with MSMT-CSD compared to SSST-CSD.

YNIMG Journal 2014 Journal Article

Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography

Thijs Dhollander
Louise Emsell
Wim Van Hecke
Frederik Maes
Stefan Sunaert
Paul Suetens

Ever since the introduction of the concept of fiber tractography, methods to generate better and more plausible tractograms have become available. Many modern methods can handle complex fiber architecture and take on a probabilistic approach to account for different sources of uncertainty. The resulting tractogram from any such method typically represents a finite random sample from a complex distribution of possible tracks. Generating a higher amount of tracks allows for a more accurate depiction of the underlying distribution. The recently proposed method of track-density imaging (TDI) allows to capture the spatial distribution of a tractogram. In this work, we propose an extension of TDI towards the 5D spatio-angular domain, which we name track orientation density imaging (TODI). The proposed method aims to capture the full track orientation distribution (TOD). Just as the TDI map, the TOD is amenable to spatial super-resolution (or even sub-resolution), but in addition also to angular super-resolution. Through experiments on in vivo human subject data, an in silico numerical phantom and a challenging tractography phantom, we found that the TOD presents an increased amount of regional spatio-angular consistency, as compared to the fiber orientation distribution (FOD) from constrained spherical deconvolution (CSD). Furthermore, we explain how the amplitude of the TOD of a short-tracks distribution (i. e. where the track length is limited) can be interpreted as a measure of track-like local support (TLS). This in turn motivated us to explore the idea of TOD-based fiber tractography. In such a setting, the short-tracks TOD is able to guide a track along directions that are more likely to correspond to continuous structure over a longer distance. This powerful concept is shown to greatly robustify targeted as well as whole-brain tractography. We conclude that the TOD is a versatile tool that can be cast in many different roles and scenarios in the expanding domain of fiber tractography based methods and their applications.