Group analysis of DTI fiber tract statistics with application to neurodevelopment

Methodological considerations on diffusion MRI tractography in infants aged 0-2 years: a scoping review

Diffusion MRI (dMRI) enables studying the complex architectural organization of the brain's white matter (WM) through virtual reconstruction of WM fiber tracts (tractography). Despite the anticipated clinical importance of applying tractography to study structural connectivity and tract development during the critical period of rapid infant brain maturation, detailed descriptions on how to approach tractography in young infants are limited. Over the past two decades, tractography from infant dMRI has mainly been applied in research settings and focused on diffusion tensor imaging (DTI). Only few studies used techniques superior to DTI in terms of disentangling information on the brain's organizational complexity, including crossing fibers. While more advanced techniques may enhance our understanding of the intricate processes of normal and abnormal brain development and extensive knowledge has been gained from application on adult scans, their applicability in infants has remained underexplored. This may partially be due to the higher technical requirements versus the need to limit scan time in young infants. We review various previously described methodological practices for tractography in the infant brain (0-2 years-of-age) and provide recommendations to optimize advanced tractography approaches to enable more accurate reconstructions of the brain WM's complexity. IMPACT: Diffusion tensor imaging is the technique most frequently used for fiber tracking in the developing infant brain but is limited in capability to disentangle the complex white matter organization. Advanced tractography techniques allow for reconstruction of crossing fiber bundles to better reflect the brain's complex organization. Yet, they pose practical and technical challenges in the fast developing young infant's brain. Methods on how to approach advanced tractography in the young infant's brain have hardly been described. Based on a literature review, recommendations are provided to optimize tractography for the developing infant brain, aiming to advance early diagnosis and neuroprotective strategies.

Fetal development of the human amygdala

The intricate development of the human amygdala involves a complex interplay of diverse processes, varying in speed and duration. In humans, transient cytoarchitectural structures deliquesce, leading to the formation of functionally distinct nuclei as a result of multiple interdependent developmental events. This study compares the amygdala's cytoarchitectural development in conjunction with specific antibody reactivity for neuronal, glial, neuropil, and radial glial fibers, synaptic, extracellular matrix, and myelin components in 39 fetal human brains. We recognized that the early fetal period, as a continuation of the embryonic period, is still dominated by relatively uniform histogenetic processes. The typical appearance of ovoid cell clusters in the lateral nucleus during midfetal period is most likely associated with the cell migration and axonal growth processes in the developing human brain. Notably, synaptic markers are firstly detected in the corticomedial group of nuclei, while immunoreactivity for the panaxonal neurofilament marker SMI 312 is found dorsally. The late fetal period is characterized by a protracted migration process evidenced by the presence of doublecortin and SOX-2 immunoreactivity ventrally, in the prospective paralaminar nucleus, reinforced by vimentin immunoreactivity in the last remaining radial glial fibers. Nearing the term period, SMI 99 immunoreactivity indicates that perinatal myelination becomes prominent primarily along major axonal pathways, laying the foundation for more pronounced functional maturation. This study comprehensively elucidates the rate and sequence of maturational events in the amygdala, highlighting the key role of prenatal development in its behavioral, autonomic, and endocrine regulation, with subsequent implications for both normal functioning and psychiatric disorders.

Lateralization of major white matter tracts during infancy is time-varying and tract-specific

Lateralization patterns are a major structural feature of brain white matter and have been investigated as a neural architecture that indicates and supports the specialization of cognitive processing and observed behaviors, e.g. language skills. Many neurodevelopmental disorders have been associated with atypical lateralization, reinforcing the need for careful measurement and study of this structural characteristic. Unfortunately, there is little consensus on the direction and magnitude of lateralization in major white matter tracts during the first months and years of life-the period of most rapid postnatal brain growth and cognitive maturation. In addition, no studies have examined white matter lateralization in a longitudinal pediatric sample-preventing confirmation of if and how white matter lateralization changes over time. Using a densely sampled longitudinal data set from neurotypical infants aged 0-6 months, we aim to (i) chart trajectories of white matter lateralization in 9 major tracts and (ii) link variable findings from cross-sectional studies of white matter lateralization in early infancy. We show that patterns of lateralization are time-varying and tract-specific and that differences in lateralization results during this period may reflect the dynamic nature of lateralization through development, which can be missed in cross-sectional studies.

Brain recovery of the NAc fibers and prediction of craving changes in person with heroin addiction: A longitudinal study

BACKGROUND

Progress have been made in brain function recovery after long-term abstinence in person with heroin addiction (PHA). However, less is known about whether the nucleus accumbens (NAc) white matter pathways can recover in PHA by prolonged abstinence.

METHODS

Forty-two PHA and Thirty-nine age- and gender- matched healthy controls (HCs) were recruited. Two MRI scans were obtained at baseline (PHA1) and 8-month follow-up (PHA2). We employed tractography atlas-based analysis (TABS) method to investigate fractional anisotropy (FA) changes in NAc fiber tracts (i.e., Insula-NAc, ventral tegmental area (VTA)-NAc, medial prefrontal cortex (MPFC)-NAc) in PHA. A partial least square regression (PLSR) analysis was carried to explore whether FA of NAc fiber tracts can predict longitudinal craving changes.

RESULTS

Relative to HCs, lower FA was found in the right Insula-NAc and VTA-NAc fiber tracts in PHA1, and PHA2 showed increased FA values in these tracts compared with PHA1. Furthermore, changes of FA of NAc fiber tracts can predict longitudinal craving changes (r = 0.51). Additionally, craving changes can also be predicted from FA changes in the left Insula-NAc (r = 0.601) and VTA-NAc (r = 0.384) fiber alone.

CONCLUSIONS

Results indicated that the right Insula-NAc and VTA-NAc fiber tracts are potential biomarkers for brain recovery. Prediction of craving changes highlighted the utility of structural markers to inform clinical decision-making of treatment for PHA.

Harmonization of Multi-Center Diffusion Tensor Tractography in Neonates with Congenital Heart Disease: Optimizing Post-Processing and Application of ComBat

Advanced brain imaging of neonatal macrostructure and microstructure, which has prognosticating importance, is more frequently being incorporated into multi-center trials of neonatal neuroprotection. Multicenter neuroimaging studies, designed to overcome small sample sized clinical cohorts, are essential but lead to increased technical variability. Few harmonization techniques have been developed for neonatal brain microstructural (diffusion tensor) analysis. The work presented here aims to remedy two common problems that exist with the current state of the art approaches: 1) variance in scanner and protocol in data collection can limit the researcher's ability to harmonize data acquired under different conditions or using different clinical populations. 2) The general lack of objective guidelines for dealing with anatomically abnormal anatomy and pathology. Often, subjects are excluded due to subjective criteria, or due to pathology that could be informative to the final analysis, leading to the loss of reproducibility and statistical power. This proves to be a barrier in the analysis of large multi-center studies and is a particularly salient problem given the relative scarcity of neonatal imaging data. We provide an objective, data-driven, and semi-automated neonatal processing pipeline designed to harmonize compartmentalized variant data acquired under different parameters. This is done by first implementing a search space reduction step of extracting the along-tract diffusivity values along each tract of interest, rather than performing whole-brain harmonization. This is followed by a data-driven outlier detection step, with the purpose of removing unwanted noise and outliers from the final harmonization. We then use an empirical Bayes harmonization algorithm performed at the along-tract level, with the output being a lower dimensional space but still spatially informative. After applying our pipeline to this large multi-site dataset of neonates and infants with congenital heart disease (n= 398 subjects recruited across 4 centers, with a total of n=763 MRI pre-operative/post-operative time points), we show that infants with single ventricle cardiac physiology demonstrate greater white matter microstructural alterations compared to infants with bi-ventricular heart disease, supporting what has previously been shown in literature. Our method is an open-source pipeline for delineating white matter tracts in subject space but provides the necessary modular components for performing atlas space analysis. As such, we validate and introduce Diffusion Imaging of Neonates by Group Organization (DINGO), a high-level, semi-automated framework that can facilitate harmonization of subject-space tractography generated from diffusion tensor imaging acquired across varying scanners, institutions, and clinical populations. Datasets acquired using varying protocols or cohorts are compartmentalized into subsets, where a cohort-specific template is generated, allowing for the propagation of the tractography mask set with higher spatial specificity. Taken together, this pipeline can reduce multi-scanner technical variability which can confound important biological variability in relation to neonatal brain microstructure.

The Brain and Early Experience Study: Protocol for a Prospective Observational Study

BACKGROUND

Children raised in conditions of poverty (or near poverty) are at risk for nonoptimal mental health, educational, and occupational outcomes, many of which may be precipitated by individual differences in executive function (EF) skills that first emerge in early childhood.

OBJECTIVE

The Brain and Early Experience study considers prenatal and postnatal experiences that may mediate the association between poverty and EF skills, including neural substrates. This paper described the study rationale and aims; research design issues, including sample size determination, the recruitment strategy, and participant characteristics; and a summary of developmental assessment points, procedures, and measures used to test the study hypotheses.

METHODS

This is a prospective longitudinal study examining multiple pathways by which poverty influences normative variations in EF skills in early childhood. It is funded by the National Institute of Child Health and Human Development and approved by the institutional review board.

RESULTS

Recruitment is complete with a sample of 203 participants, and data collection is expected to continue from September 2018 to February 2024. Of those recruited as low socioeconomic status (SES), 71% (55/78) reported income-to-needs (ITN) ratios of <2.0, and 35% (27/78) reported ITN ratios of <1.0. Among participants recruited into the not-low SES stratum, only 8.8% (11/125) reported ITN ratios of <2.0, and no participant reported ITN ratios of <1.0. The average ITN ratio for participants recruited into the low-income stratum was significantly lower than the average for the high-income recruitment cell (P<.001). Comparable recruitment outcomes were observed for both Black and non-Black families. Overall, the sample has adequate diversity for testing proposed hypotheses, with 13.3% (27/203) of participants reporting ITN ratios of <1 and >32.5% (66/203) reporting ratios of <2.0.

CONCLUSIONS

Preliminary results indicate that the recruitment strategy for maximizing variation in family SES was successful, including variation within race. The findings of this study will help elucidate the complex interplay between prenatal and postnatal risk factors affecting critical neurocognitive developmental outcomes in early childhood.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/34854.

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: A review

Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain's white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain's structural connectivity using measures of connectivity or tissue microstructure. Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape. In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease. We focus on two types of quantitative analyses of tractography, including: 1) tract-specific analysis that refers to research that is typically hypothesis-driven and studies particular anatomical fiber tracts, and 2) connectome-based analysis that refers to research that is more data-driven and generally studies the structural connectivity of the entire brain. We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction, segmentation and quantification. For each step, we aim to describe methodological choices, their popularity, and potential pros and cons. We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders, and neurosurgery. We conclude that, while there have been considerable advancements in methodological technologies and breadth of applications, there nevertheless remains no consensus about the "best" methodology in quantitative analysis of tractography, and researchers should remain cautious when interpreting results in research and clinical applications.

Diffusion Tensor Based White Matter Tract Atlases for Pediatric Populations

Diffusion Tensor Imaging (DTI) is a non-invasive neuroimaging method that has become the most widely employed MRI modality for investigations of white matter fiber pathways. DTI has proven especially valuable for improving our understanding of normative white matter maturation across the life span and has also been used to index clinical pathology and cognitive function. Despite its increasing popularity, especially in pediatric research, the majority of existing studies examining infant white matter maturation depend on regional or white matter skeleton-based approaches. These methods generally lack the sensitivity and spatial specificity of more advanced functional analysis options that provide information about microstructural properties of white matter along fiber bundles. DTI studies of early postnatal brain development show that profound microstructural and maturational changes take place during the first two years of life. The pattern and rate of these changes vary greatly throughout the brain during this time compared to the rest of the life span. For this reason, appropriate image processing of infant MR imaging requires the use of age-specific reference atlases. This article provides an overview of the pre-processing, atlas building, and the fiber tractography procedures used to generate two atlas resources, one for neonates and one for 1- to 2-year-old populations. Via the UNC-NAMIC DTI Fiber Analysis Framework, our pediatric atlases provide the computational templates necessary for the fully automatic analysis of infant DTI data. To the best of our knowledge, these atlases are the first comprehensive population diffusion fiber atlases in early pediatric ages that are publicly available.

Tract Specific White Matter Lesion Load Affects White Matter Microstructure and Their Relationships With Functional Connectivity and Cognitive Decline

White matter hyperintensities (WMHs) are associated with cognitive decline. Assessing the effect of WMH on WM microstructural changes and its relationships with structural and functional connectivity to multiple cognitive domains are helpful to better understand the pathophysiological processes of cognitive impairment. 65 participants (49 normal and 16 MCI subjects, age: 67.4 ± 8.3 years, 44 females) were studied at 3T. The WMHs and fifty fiber tracts were automatically segmented from the T1/T2-weighted images and diffusion-weighted images, respectively. Tract-profiles of WMH were compared with those of apparent fiber density (AFD). The relationship between AFD and tract connectivity (TC) was assessed. Functional connectivity (FC) between tract ends obtained from resting-state functional MRI was examined in relation to TC. Tract-specific relationships of WMH, TC and FC with a multi-domain neuropsychological test battery and Montreal Cognitive Assessment (MoCA) were also separately assessed by lasso linear regression. Indirect pathways of TC and FC between WMH and multiple cognitive measures were tested using the mediation analysis. Higher WMH loads in WM tracts were locally matched with the reduced AFD, which was related to decrease in TC. However, no direct relationship was found between TC and FC. Tract-specific changes on WMH, TC and FC for each cognitive performance may explain that macro- and microstructural and functional changes are associated differently with each cognitive domain in a fiber specific manner. In these identified tracts, the differences between normal and MCI for WMH and TC were increased, and the relationships of WMH, TC and FC with cognitive outcomes were more significant, compared to the results from all tracts. Indirect pathways of two-step (TC-FC) between WMH and all cognitive domains were significant (p < 0.0083 with Bonferroni correction), while the separated indirect pathways through TC and through FC were different depending on cognitive domain. Deterioration in specific cognitive domains may be affected by alterations in a set of different tracts that are differently associated with macrostructural, microstructural, and function changes. Thus, assessments of WMH and its associated changes on specific tracts help for better understanding of the interrelationships of multiple changes in cognitive impairment.

Along-tract analysis of the white matter is more informative about brain ageing, compared to whole-tract analysis

Diffusion Tensor Imaging (DTI) enabled the investigation of brain White Matter (WM), both qualitatively to study the macrostructure, and quantitatively to study the microstructure. The quantitative analyses are mostly performed at the whole-tract level, i.e., providing one measure of interest per tract; however, along-tract approaches may provide finer details of the quality of the WM tracts. In this study, using the DWI data collected from 40 young and 40 old individuals, we compared the DTI measures of FA, MD, AD, and RD, estimated by both whole-tract and along-tract approaches in 18 WM bundles, between the two groups. The results of the whole-tract quantitative analysis showed a statistically significant (p-FWER < 0.05) difference between the old and young groups in 6 tracts for FA, 8 tracts for MD, 1 tract for AD, and 7 tracts for RD. On the contrary, the along-tract approach showed differences between the two groups in 10 tracts for FA, 14 tracts for MD, 8 tracts for AD, and 11 tracts for RD. All the differences between the along-tract measures of the two groups had a large effect size (Cohen'd > 0.80). This study showed that the along-tract approach for the analysis of brain WM reveals changes in some WM tracts which had not shown any changes in the whole-tract approach, and therefore this finding emphasizes the utilization of the along-tract approach along with the whole-tract method for a more accurate study of the brain WM.

Differential White Matter Maturation from Birth to 8 Years of Age

Comprehensive delineation of white matter (WM) microstructural maturation from birth to childhood is critical for understanding spatiotemporally differential circuit formation. Without a relatively large sample of datasets and coverage of critical developmental periods of both infancy and early childhood, differential maturational charts across WM tracts cannot be delineated. With diffusion tensor imaging (DTI) of 118 typically developing (TD) children aged 0–8 years and 31 children with autistic spectrum disorder (ASD) aged 2–7 years, the microstructure of every major WM tract and tract group was measured with DTI metrics to delineate differential WM maturation. The exponential model of microstructural maturation of all WM was identified. The WM developmental curves were separated into fast, intermediate, and slow phases in 0–8 years with distinctive time period of each phase across the tracts. Shorter periods of the fast and intermediate phases in certain tracts, such as the commissural tracts, indicated faster earlier development. With TD WM maturational curves as the reference, higher residual variance of WM microstructure was found in children with ASD. The presented comprehensive and differential charts of TD WM microstructural maturation of all major tracts and tract groups in 0–8 years provide reference standards for biomarker detection of neuropsychiatric disorders.

Fascicle- and Glucose-Specific Deterioration in White Matter Energy Supply in Alzheimer's Disease

BACKGROUND

White matter energy supply to oligodendrocytes and the axonal compartment is crucial for normal axonal function. Although gray matter glucose hypometabolism is extensively reported in Alzheimer's disease (AD), glucose and ketones, the brain's two main fuels, are rarely quantified in white matter in AD.

OBJECTIVE

Using a dual-tracer PET method combined with a fascicle-specific diffusion MRI approach, robust to white matter hyper intensities and crossing fibers, we aimed to quantify both glucose and ketone metabolism in specific white matter fascicles associated with mild cognitive impairment (MCI; n = 51) and AD (n = 13) compared to cognitively healthy age-matched controls (Controls; n = 14).

METHODS

Eight white matter fascicles of the limbic lobe and corpus callosum were extracted and analyzed into fascicle profiles of five sections. Glucose (18F-fluorodeoxyglucose) and ketone (11C-acetoacetate) uptake rates, corrected for partial volume effect, were calculated along each fascicle.

RESULTS

The only fascicle with significantly lower glucose uptake in AD compared to Controls was the left posterior cingulate segment of the cingulum (-22%; p = 0.016). Non-significantly lower glucose uptake in this fascicle was also observed in MCI. In contrast to glucose, ketone uptake was either unchanged or higher in sections of the fornix and parahippocampal segment of the cingulum in AD.

CONCLUSION

To our knowledge, this is the first report of brain fuel uptake calculated along white matter fascicles in humans. Energetic deterioration in white matter in AD appears to be specific to glucose and occurs first in the posterior cingulum.

Diffusion Tensor Imaging Group Analysis Using Tract Profiling and Directional Statistics

Group analysis in diffusion tensor imaging is challenging. Comparisons of tensor morphology across groups have typically been performed on scalar measures of diffusivity, such as fractional anisotropy (FA), disregarding the complex three-dimensional morphologies of diffusion tensors. Scalar measures consider only the magnitude of the diffusion but not directions. In the present study, we have introduced a new approach based on directional statistics to use directional information of diffusion tensors in statistical group analysis based on Bingham distribution. We have investigated different directional statistical models to find the best fit. During the experiments, we confirmed that carrying out directional statistical analysis along the tract is much more effective than voxel- or skeleton-guided directional statistics. Hence, we propose a new method called tract profiling and directional statistics (TPDS) applicable to fiber bundles. As a case study, the method has been applied to identify connectivity differences of patients with major depressive disorder. The results obtained with the directional statistic-based analysis are consistent with those of NBS, but additionally, we found significant changes in the right hemisphere striatum, ACC, and prefrontal, parietal, temporal, and occipital connections as well as left hemispheric differences in the limbic areas such as the thalamus, amygdala, and hippocampus. The results are also evaluated with respect to fiber lengths. Comparison with the output of the network-based statistical toolbox indicated that the benefit of the proposed method becomes much more distinctive as the tract length increases. The likelihood of finding clusters of voxels that differ in long tracts is higher in TPDS, while that relationship is not clearly established in NBS.

Genome-Wide Association Analysis of Neonatal White Matter Microstructure

A better understanding of genetic influences on early white matter development could significantly advance our understanding of neurological and psychiatric conditions characterized by altered integrity of axonal pathways. We conducted a genome-wide association study (GWAS) of diffusion tensor imaging (DTI) phenotypes in 471 neonates. We used a hierarchical functional principal regression model (HFPRM) to perform joint analysis of 44 fiber bundles. HFPRM revealed a latent measure of white matter microstructure that explained approximately 50% of variation in our tractography-based measures and accounted for a large proportion of heritable variation in each individual bundle. An intronic SNP in PSMF1 on chromosome 20 exceeded the conventional GWAS threshold of 5 x 10-8 (p = 4.61 x 10-8). Additional loci nearing genome-wide significance were located near genes with known roles in axon growth and guidance, fasciculation, and myelination.

Diffusion magnetic resonance imaging assessment of regional white matter maturation in preterm neonates

Purpose

Diffusion magnetic resonance imaging (dMRI) studies report altered white matter (WM) development in preterm infants. Neurite orientation dispersion and density imaging (NODDI) metrics provide more realistic estimations of neurite architecture in vivo compared with standard diffusion tensor imaging (DTI) metrics. This study investigated microstructural maturation of WM in preterm neonates scanned between 25 and 45 weeks postmenstrual age (PMA) with normal neurodevelopmental outcomes at 2 years using DTI and NODDI metrics.

Methods

Thirty-one neonates (n = 17 male) with median (range) gestational age (GA) 32⁺¹ weeks (24⁺²–36⁺⁴) underwent 3 T brain MRI at median (range) post menstrual age (PMA) 35⁺² weeks (25⁺³–43⁺¹). WM tracts (cingulum, fornix, corticospinal tract (CST), inferior longitudinal fasciculus (ILF), optic radiations) were delineated using constrained spherical deconvolution and probabilistic tractography in MRtrix3. DTI and NODDI metrics were extracted for the whole tract and cross-sections along each tract to assess regional development.

Results

PMA at scan positively correlated with fractional anisotropy (FA) in the CST, fornix and optic radiations and neurite density index (NDI) in the cingulum, CST and fornix and negatively correlated with mean diffusivity (MD) in all tracts. A multilinear regression model demonstrated PMA at scan influenced all diffusion measures, GA and GAxPMA at scan influenced FA, MD and NDI and gender affected NDI. Cross-sectional analyses revealed asynchronous WM maturation within and between WM tracts.).

Conclusion

We describe normal WM maturation in preterm neonates with normal neurodevelopmental outcomes. NODDI can enhance our understanding of WM maturation compared with standard DTI metrics alone.

Supplementary Information

The online version of this article (10.1007/s00234-020-02584-9) contains supplementary material, which is available to authorized users.

Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations

Tractography has created new horizons for researchers to study brain connectivity in vivo. However, tractography is an advanced and challenging method that has not been used so far for medical data analysis at a large scale in comparison to other traditional brain imaging methods. This work allows tractography to be used for large scale and high-quality medical analytics. BUndle ANalytics (BUAN) is a fast, robust, and flexible computational framework for real-world tractometric studies. BUAN combines tractography and anatomical information to analyze the challenging datasets and identifies significant group differences in specific locations of the white matter bundles. Additionally, BUAN takes the shape of the bundles into consideration for the analysis. BUAN compares the shapes of the bundles using a metric called bundle adjacency which calculates shape similarity between two given bundles. BUAN builds networks of bundle shape similarities that can be paramount for automating quality control. BUAN is freely available in DIPY. Results are presented using publicly available Parkinson's Progression Markers Initiative data.

Abnormal white matter microstructure along the thalamus fiber pathways in women with primary dysmenorrhea

Primary dysmenorrhea (PDM) is a cyclic menstrual pain in the absence of pelvic anomalies, and women with PDM have an increased sensitivity to pain than the internal and external areas associated with menstrual pain. However, the brain abnormality in the ascending pain pathways in dysmenorrhea remains largely unclear. As the thalamus plays a significant role in transmission of nociceptive input, we examined whether white matter microstructure of the thalamus-related fiber tracts obtained by DTI in women with PDM (n = 47) differs from healthy controls. A novel tractography atlas-based analysis method that detects tract integrity and altered microstructural properties along selected fibers was employed. The fiber bundles of interest contained the thalamus- primary somatosensory cortex (SI), thalamus- dorsal anterior cingulate cortex (dACC)/supplementary motor area (SMA), thalamus-insula, and thalamus-ACC. As compared with controls, abnormal white matter microstructures were found along the thalamus-related white matter fiber tracts. Additionally, the intensity of menstrual pain was significantly associated with diffusion measures of thalamus-SI fiber connections. Our study suggested that the thalamus-related pain processing pathways had altered white matter integrity that persisted beyond the time of menstruation, and the white matter microstructure of the thalamus-SI pathways was closely related to menstrual pain in the intensity by women with PDM.

Automatic, Age Consistent Reconstruction of the Corpus Callosum Guided by Coherency From In Utero Diffusion-Weighted MRI

Reconstruction of white matter connectivity in the fetal brain from in utero diffusion-weighted magnetic resonance imaging (MRI) faces many challenges, including subject motion, small anatomical scale, and limited image resolution and signal. These issues are compounded by the need to track significant changes in structural connectivity throughout development. We present an automated method for improved reliability and completeness of tract extraction across a wide range of gestational ages, based on the geometry of coherent patterns in streamline tractography, and apply it to the reconstruction of the corpus callosum. This method, focused specifically at addressing the challenges of fetal brain imaging, avoids depending on a tractography atlas, and handles variations in size, shape, and tissue properties of developing brains, both between subjects and across ages. Although tractography from in utero MRI generally suffers from a significant number of misleading and missing pathways, we demonstrate the feasibility of extracting the coherent bundle of the corpus callosum while avoiding inappropriate diversions into other tracts.

Magnitude and timing of major white matter tract maturation from infancy through adolescence with NODDI

White matter maturation is a nonlinear and heterogeneous phenomenon characterized by axonal packing, increased axon caliber, and a prolonged period of myelination. While current in vivo diffusion MRI (dMRI) methods, like diffusion tensor imaging (DTI), have successfully characterized the gross structure of major white matter tracts, these measures lack the specificity required to unravel the distinct processes that contribute to microstructural development. Neurite orientation dispersion and density imaging (NODDI) is a dMRI approach that probes tissue compartments and provides biologically meaningful measures that quantify neurite density index (NDI) and orientation dispersion index (ODI). The purpose of this study was to characterize the magnitude and timing of major white matter tract maturation with NODDI from infancy through adolescence in a cross-sectional cohort of 104 subjects (0.6–18.8 years). To probe the regional nature of white matter development, we use an along-tract approach that partitions tracts to enable more fine-grained analysis. Major white matter tracts showed exponential age-related changes in NDI with distinct maturational patterns. Overall, analyses revealed callosal fibers developed before association fibers. Our along-tract analyses elucidate spatially varying patterns of maturation with NDI that are distinct from those obtained with DTI. ODI was not significantly associated with age in the majority of tracts. Our results support the conclusion that white matter tract maturation is heterochronous process and, furthermore, we demonstrate regional variability in the developmental timing within major white matter tracts. Together, these results help to disentangle the distinct processes that contribute to and more specifically define the time course of white matter maturation.

A framework to construct a longitudinal DW-MRI infant atlas based on mixed effects modeling of dODF coefficients

Building of atlases plays a crucial role in the analysis of brain images. In scenarios where early growth, aging or disease trajectories are of key importance, longitudinal atlases become necessary as references, most often created from cross-sectional data. New opportunities will be offered by creating longitudinal brain atlases from longitudinal subject-specific image data, where explicit modeling of subject's variability in slope and intercept leads to a more robust estimation of average trajectories but also to estimates of confidence bounds. This work focuses on a framework to build a continuous 4D atlas from longitudinal high angular resolution diffusion images (HARDI) where, unlike atlases of derived scalar diffusion indices such as FA, statistics on dODFs is preserved. Multi-scalar images obtained from DW images are used for geometric alignment, and linear mixed-effects modeling from longitudinal diffusion orientation distribution functions (dODF) leads to estimation of continuous dODF changes. The proposed method is applied to a longitudinal dataset of HARDI images from healthy developing infants in the age range of 3 to 36 months. Verification of mixed-effects modeling is obtained by voxel-wise goodness of fit calculations. To demonstrate the potential of our method, we display changes of longitudinal atlas using dODF and derived generalized fractional anisotropy (GFA) of dODF. We also investigate white matter maturation patterns in genu, body, and splenium of the corpus callosum. The framework can be used to build an average dODF atlas from HARDI data and to derive subject-specific and population-based longitudinal change trajectories.

White matter development in infants at risk for schizophrenia

BACKGROUND

Schizophrenia is considered a neurodevelopmental disorder with a pathophysiology that likely begins long before the onset of clinical symptoms. White matter abnormalities have been observed in schizophrenia and we hypothesized that the first 2 years of life is a period in which white matter abnormalities associated with schizophrenia risk may emerge.

METHODS

38 infants at high risk for schizophrenia and 202 healthy controls underwent diffusion tensor MRIs after birth and at 1 and 2 years of age. Quantitative tractography was used to determine diffusion properties (fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD)) of 18 white matter tracts and a general linear model was used to analyze group differences at each age.

RESULTS

Adjusting gestational age at birth, postnatal age at MRI, gender, MRI scanner type, and maternal education, neonates at high risk had significantly lower FA (p = 0.02) and AD (p = 0.03) in the superior segment of the left cingulate, and higher RD in the hippocampal segment of the left cingulate (p = 0.04). High risk one year olds had significantly lower FA (p < 0.01) and AD (p = 0.02) in the hippocampal segment of the left cingulate. High risk two year olds had significantly lower FA in the left prefrontal cortico-thalamic tract (p = 0.04) and higher RD in the right uncinate fasciculus (p = 0.04). None of the tract differences remained significant after correction for multiple comparisons.

CONCLUSIONS

There is evidence of abnormal white matter development in young children at risk for schizophrenia, especially in the hippocampal segment of left cingulum. These results support the neurodevelopmental theory of schizophrenia and indicate that impaired white matter may be present in early childhood.

Subgroup identification via homogeneity pursuit for dense longitudinal/spatial data

In the clinical trial community, it is usually not easy to find a treatment that benefits all patients since the reaction to treatment may differ substantially across different patient subgroups. The heterogeneity of treatment effect plays an essential role in personalized medicine. To facilitate the development of tailored therapies and improve the treatment efficacy, it is important to identify subgroups that exhibit different treatment effects. We consider a very general framework for subgroup identification via the homogeneity pursuit methods usually employed in econometric time series analysis. The change point detection algorithm in our procedure is most suitable for analyzing dense longitudinal or spatial data which are quite common for biomedical studies these days. We demonstrate that our proposed method is fast and accurate through extensive numerical studies. In particular, our method is illustrated by analyzing a diffusion tensor imaging data set.

Dimensionality reduction of diffusion MRI measures for improved tractometry of the human brain

Various diffusion MRI (dMRI) measures have been proposed for characterising tissue microstructure over the last 15 years. Despite the growing number of experiments using different dMRI measures in assessments of white matter, there has been limited work on: 1) examining their covariance along specific pathways; and on 2) combining these different measures to study tissue microstructure. Indeed, it quickly becomes intractable for existing analysis pipelines to process multiple measurements at each voxel and at each vertex forming a streamline, highlighting the need for new ways to visualise or analyse such high-dimensional data. In a sample of 36 typically developing children aged 8–18 years, we profiled various commonly used dMRI measures across 22 brain pathways. Using a data-reduction approach, we identified two biologically-interpretable components that capture 80% of the variance in these dMRI measures. The first derived component captures properties related to hindrance and restriction in tissue microstructure, while the second component reflects characteristics related to tissue complexity and orientational dispersion. We then demonstrate that the components generated by this approach preserve the biological relevance of the original measurements by showing age-related effects across developmentally sensitive pathways. In summary, our findings demonstrate that dMRI analyses can benefit from dimensionality reduction techniques, to help disentangling the neurobiological underpinnings of white matter organisation.

Quantitative tract-based white matter heritability in 1- and 2-year-old twins

White matter (WM) microstructure, as determined by diffusion tensor imaging (DTI), is increasingly recognized as an important determinant of cognitive function and is also altered in neuropsychiatric disorders. Little is known about genetic and environmental influences on WM microstructure, especially in early childhood, an important period for cognitive development and risk for psychiatric disorders. We studied the heritability of DTI parameters, fractional anisotropy (FA), radial diffusivity (RD) and axial diffusivity (AD) along 34 tracts, including 10 bilateral fiber pathways and the respective subdivision, using quantitative tractography in a longitudinal sample of healthy children at 1 year (N = 215) and 2 years (N = 165) of age. We found that heritabilities for whole brain AD, RD, and FA were 0.48, 0.69, and 0.72 at age 1, and 0.59, 0.77, and 0.76 at age 2 and that mean heritabilities of tract-averaged AD, RD, and FA for individual bundles were moderate (over 0.4). However, the heritability of DTI change between 1 and 2 years of age was not significant for most tracts. We also demonstrated that point-wise heritability tended to be significant in the central portions of the tracts and was generally spatially consistent at ages 1 and 2 years. These results, especially when compared to heritability patterns in neonates, indicate that the heritability of WM microstructure is dynamic in early childhood and likely reflect heterogeneous maturation of WM tracts and differential genetic and environmental influences on maturation patterns.

White matter microstructural development and cognitive ability in the first 2 years of life

White matter (WM) integrity has been related to cognitive ability in adults and children, but it remains largely unknown how WM maturation in early life supports emergent cognition. The associations between tract-based measures of fractional anisotropy (FA) and axial and radial diffusivity (AD, RD) shortly after birth, at age 1, and at age 2 and cognitive measures at 1 and 2 years were investigated in 447 healthy infants. We found that generally higher FA and lower AD and RD across many WM tracts in the first year of life were associated with better performance on measures of general cognitive ability, motor, language, and visual reception skills at ages 1 and 2, suggesting an important role for the overall organization, myelination, and microstructural properties of fiber pathways in emergent cognition. RD in particular was consistently related to ability, and protracted development of RD from ages 1 to 2 years in several tracts was associated with higher cognitive scores and better language performance, suggesting prolonged plasticity may confer cognitive benefits during the second year of life. However, we also found that cognition at age 2 was weakly associated with WM properties across infancy in comparison to child and demographic factors including gestational age and maternal education. Our findings suggest that early postnatal WM integrity across the brain is important for infant cognition, though its role in cognitive development should be considered alongside child and demographic factors.

Impact of white matter hyperintensities on surrounding white matter tracts

PURPOSE

It is unclear how white matter hyperintensities disrupt surrounding white matter tracts. The aim of this tractography study was to determine the spatial relationship between diffusion characteristics along white matter tracts and the distance from white matter hyperintensities.

METHODS

Diffusion tensor 3-T MRI scans were acquired in 29 participants with white matter hyperintensities. In each subject, tractography by the fiber assignment by continuous tracking method was used to segment corticospinal tracts. Mean diffusivity, radial diffusivity, axial diffusivity, and fractional anisotropy were measured along corticospinal tracts in relation to white matter hyperintensities. Diffusion characteristics along tracts were correlated with distance from white matter hyperintensities and were also compared between tracts traversing and not traversing white matter hyperintensities.

RESULTS

In tracts not traversing through white matter hyperintensities, increasing distance from white matter hyperintensities was associated with decreased mean diffusivity (p = 0.002) and increased fractional anisotropy (p = 0.006). In tracts traversing white matter hyperintensities, compared to tracts not traversing white matter hyperintensites, the mean diffusivity was higher at 6-8 voxels, axial diffusivity higher at 4-8 voxels, and radial diffusivity higher at 7 voxels away from white matter hyperintensities (all p < 0.006).

CONCLUSION

White matter hyperintensities are associated with two patterns of altered diffusion characteristics in the surrounding white matter tract network. Diffusion characteristics along white matter tracts improve further away from white matter hyperintensities suggestive of a local penumbra pattern. Also, altered diffusion extends further along tracts traversing white matter hyperintensities suggestive of a Wallerian-type degenerative pattern.

FSEM: Functional Structural Equation Models for Twin Functional Data

The aim of this paper is to develop a novel class of functional structural equation models (FSEMs) for dissecting functional genetic and environmental effects on twin functional data, while characterizing the varying association between functional data and covariates of interest. We propose a three-stage estimation procedure to estimate varying coefficient functions for various covariates (e.g., gender) as well as three covariance operators for the genetic and environmental effects. We develop an inference procedure based on weighted likelihood ratio statistics to test the genetic/environmental effect at either a fixed location or a compact region. We also systematically carry out the theoretical analysis of the estimated varying functions, the weighted likelihood ratio statistics, and the estimated covariance operators. We conduct extensive Monte Carlo simulations to examine the finite-sample performance of the estimation and inference procedures. We apply the proposed FSEM to quantify the degree of genetic and environmental effects on twin white-matter tracts obtained from the UNC early brain development study.

The journey to autism: Insights from neuroimaging studies of infants and toddlers

By definition, autism spectrum disorder (ASD) is a neurodevelopmental disorder that emerges during early childhood. It is during this time that infants and toddlers transition from appearing typical across multiple domains to exhibiting the behavioral phenotype of ASD. Neuroimaging studies focused on this period of development have provided crucial knowledge pertaining to this process, including possible mechanisms underlying pathogenesis of the disorder and offering the possibility of prodromal or presymptomatic prediction of risk. In this paper, we review findings from structural and functional brain imaging studies of ASD focused on the first years of life and discuss implications for next steps in research and clinical applications.

TRAFIC: Fiber Tract Classification Using Deep Learning

We present TRAFIC, a fully automated tool for the labeling and classification of brain fiber tracts. TRAFIC classifies new fibers using a neural network trained using shape features computed from previously traced and manually corrected fiber tracts. It is independent from a DTI Atlas as it is applied to already traced fibers. This work is motivated by medical applications where the process of extracting fibers from a DTI atlas, or classifying fibers manually is time consuming and requires knowledge about brain anatomy. With this new approach we were able to classify traced fiber tracts obtaining encouraging results. In this report we will present in detail the methods used and the results achieved with our approach.

A Comprehensive Atlas of E3 Ubiquitin Ligase Mutations in Neurological Disorders

Protein ubiquitination is a posttranslational modification that plays an integral part in mediating diverse cellular functions. The process of protein ubiquitination requires an enzymatic cascade that consists of a ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and an E3 ubiquitin ligase (E3). There are an estimated 600-700 E3 ligase genes representing ~5% of the human genome. Not surprisingly, mutations in E3 ligase genes have been observed in multiple neurological conditions. We constructed a comprehensive atlas of disrupted E3 ligase genes in common (CND) and rare neurological diseases (RND). Of the predicted and known human E3 ligase genes, we found ~13% were mutated in a neurological disorder with 83 total genes representing 70 different types of neurological diseases. Of the E3 ligase genes identified, 51 were associated with an RND. Here, we provide an updated list of neurological disorders associated with E3 ligase gene disruption. We further highlight research in these neurological disorders and discuss the advanced technologies used to support these findings.

Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis

This work presents a suprathreshold fiber cluster (STFC) method that leverages the whole brain fiber geometry to enhance statistical group difference analyses. The proposed method consists of 1) a well-established study-specific data-driven tractography parcellation to obtain white matter tract parcels and 2) a newly proposed nonparametric, permutation-test-based STFC method to identify significant differences between study populations. The basic idea of our method is that a white matter parcel's neighborhood (nearby parcels with similar white matter anatomy) can support the parcel's statistical significance when correcting for multiple comparisons. We propose an adaptive parcel neighborhood strategy to allow suprathreshold fiber cluster formation that is robust to anatomically varying inter-parcel distances. The method is demonstrated by application to a multi-shell diffusion MRI dataset from 59 individuals, including 30 attention deficit hyperactivity disorder patients and 29 healthy controls. Evaluations are conducted using both synthetic and in-vivo data. The results indicate that the STFC method gives greater sensitivity in finding group differences in white matter tract parcels compared to several traditional multiple comparison correction methods.

The effect of feature image on sensitivity of the statistical analysis in the pipeline of a tractography atlas-based analysis

Tractography atlas-based analysis (TABS) is a new diffusion tensor image (DTI) statistical analysis method for detecting and understanding voxel-wise white matter properties along a fiber tract. An important requisite for accurate and sensitive TABS is the availability of a deformation field that is able to register DTI in native space to standard space. Here, three different feature images including the fractional anisotropy (FA) image, T1 weighted image, and the maximum eigenvalue of the Hessian of the FA (hFA) image were used to calculate the deformation fields between individual space and population space. Our results showed that when the FA image was a feature image, the tensor template had the highest consistency with each subject for scalar and vector information. Additionally, to demonstrate the sensitivity and specificity of the TABS method with different feature images, we detected a gender difference along the corpus callosum. A significant difference between the male and female group in diffusion measurement appeared predominantly in the right corpus callosum only when FA was the feature image. Our results demonstrated that the FA image as a feature image was more accurate with respect to the underlying tensor information and had more accurate analysis results with the TABS method.

FGWAS: Functional genome wide association analysis

Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes. FGWAS consists of three components: a multivariate varying coefficient model, a global sure independence screening procedure, and a test procedure. Compared with the standard multivariate regression model, the multivariate varying coefficient model explicitly models the functional features of functional phenotypes through the integration of smooth coefficient functions and functional principal component analysis. Statistically, compared with existing methods for genome-wide association studies (GWAS), FGWAS can substantially boost the detection power for discovering important genetic variants influencing brain structure and function. Simulation studies show that FGWAS outperforms existing GWAS methods for searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. We have successfully applied FGWAS to large-scale analysis of data from the Alzheimer's Disease Neuroimaging Initiative for 708 subjects, 30,000 vertices on the left and right hippocampal surfaces, and 501,584 SNPs.

HFPRM: Hierarchical Functional Principal Regression Model for Diffusion Tensor Image Bundle Statistics

Diffusion-weighted magnetic resonance imaging (MRI) provides a unique approach to understand the geometric structure of brain fiber bundles and to delineate the diffusion properties across subjects and time. It can be used to identify structural connectivity abnormalities and helps to diagnose brain-related disorders. The aim of this paper is to develop a novel, robust, and efficient dimensional reduction and regression framework, called hierarchical functional principal regression model (HFPRM), to effectively correlate high-dimensional fiber bundle statistics with a set of predictors of interest, such as age, diagnosis status, and genetic markers. The three key novelties of HFPRM include the simultaneous analysis of a large number of fiber bundles, the disentanglement of global and individual latent factors that characterizes between-tract correlation patterns, and a bi-level analysis on the predictor effects. Simulations are conducted to evaluate the finite sample performance of HFPRM. We have also applied HFPRM to a genome-wide association study to explore important genetic variants in neonatal white matter development.

Riemannian Variance Filtering: An Independent Filtering Scheme for Statistical Tests on Manifold-valued Data

Performing large scale hypothesis testing on brain imaging data to identify group-wise differences (e.g., between healthy and diseased subjects) typically leads to a large number of tests (one per voxel). Multiple testing adjustment (or correction) is necessary to control false positives, which may lead to lower detection power in detecting true positives. Motivated by the use of so-called "independent filtering" techniques in statistics (for genomics applications), this paper investigates the use of independent filtering for manifold-valued data (e.g., Diffusion Tensor Imaging, Cauchy Deformation Tensors) which are broadly used in neuroimaging studies. Inspired by the concept of variance of a Riemannian Gaussian distribution, a type of non-specific data-dependent Riemannian variance filter is proposed. In practice, the filter will select a subset of the full set of voxels for performing the statistical test, leading to a more appropriate multiple testing correction. Our experiments on synthetic/simulated manifold-valued data show that the detection power is improved when the statistical tests are performed on the voxel locations that "pass" the filter. Given the broadening scope of applications where manifold-valued data are utilized, the scheme can serve as a general feature selection scheme.

Decreased Axon Caliber Underlies Loss of Fiber Tract Integrity, Disproportional Reductions in White Matter Volume, and Microcephaly in Angelman Syndrome Model Mice

Angelman syndrome (AS) is a debilitating neurodevelopmental disorder caused by loss of function of the maternally inherited UBE3A allele. It is currently unclear how the consequences of this genetic insult unfold to impair neurodevelopment. We reasoned that by elucidating the basis of microcephaly in AS, a highly penetrant syndromic feature with early postnatal onset, we would gain new insights into the mechanisms by which maternal UBE3A loss derails neurotypical brain growth and function. Detailed anatomical analysis of both male and female maternal Ube3a-null mice reveals that microcephaly in the AS mouse model is primarily driven by deficits in the growth of white matter tracts, which by adulthood are characterized by densely packed axons of disproportionately small caliber. Our results implicate impaired axon growth in the pathogenesis of AS and identify noninvasive structural neuroimaging as a potentially valuable tool for gauging therapeutic efficacy in the disorder.SIGNIFICANCE STATEMENT People who maternally inherit a deletion or nonfunctional copy of the UBE3A gene develop Angelman syndrome (AS), a severe neurodevelopmental disorder. To better understand how loss of maternal UBE3A function derails brain development, we analyzed brain structure in a maternal Ube3a knock-out mouse model of AS. We report that the volume of white matter (WM) is disproportionately reduced in AS mice, indicating that deficits in WM development are a major factor underlying impaired brain growth and microcephaly in the disorder. Notably, we find that axons within the WM pathways of AS model mice are abnormally small in caliber. This defect is associated with slowed nerve conduction, which could contribute to behavioral deficits in AS, including motor dysfunction.

Altered white matter microarchitecture in the cingulum bundle in women with primary dysmenorrhea: A tract-based analysis study

Primary dysmenorrhea (PD), as characterized by painful menstrual cramps without organic causes, is associated with central sensitization and brain function changes. Previous studies showed the integrated role of the default mode network (DMN) in the pain connectome and its key contribution on how an individual perceives and copes with pain disorders. Here, we aimed to investigate whether the cingulum bundle connecting hub regions of the DMN was disrupted in young women with PD. Diffusion tensor imaging was obtained in 41 PD patients and 41 matched healthy controls (HC) during their periovulatory phase. The production of prostaglandins (PGs) was obtained in PD patients during their pain-free and pain phases. As compared with HC, PD patients had similar scores of pain intensity, anxiety, and depression in their pain-free phase. However, altered white matter properties mainly located in the posterior section of the cingulum bundle were observed in PD. Besides PGs being related to menstrual pain, a close relationship was found between the white matter properties of the cingulum bundle during the pain-free phase and the severity of the menstrual pain in PD patients. Our study suggested that PD had trait changes of white matter integrities in the cingulum bundle that persisted beyond the time of menstruation. We inferred that altered anatomical connections may lead to less-flexible communication within the DMN, and/or between the DMN and other pain-related brain networks, which may result in the central susceptibility to develop chronic pain conditions in PD's later life. Hum Brain Mapp 38:4430-4443, 2017. © 2017 Wiley Periodicals, Inc.

A tract-specific approach to assessing white matter in preterm infants

Diffusion-weighted imaging (DWI) is becoming an increasingly important tool for studying brain development. DWI analyses relying on manually-drawn regions of interest and tractography using manually-placed waypoints are considered to provide the most accurate characterisation of the underlying brain structure. However, these methods are labour-intensive and become impractical for studies with large cohorts and numerous white matter (WM) tracts. Tract-specific analysis (TSA) is an alternative WM analysis method applicable to large-scale studies that offers potential benefits. TSA produces a skeleton representation of WM tracts and projects the group's diffusion data onto the skeleton for statistical analysis. In this work we evaluate the performance of TSA in analysing preterm infant data against results obtained from native space tractography and tract-based spatial statistics. We evaluate TSA's registration accuracy of WM tracts and assess the agreement between native space data and template space data projected onto WM skeletons, in 12 tracts across 48 preterm neonates. We show that TSA registration provides better WM tract alignment than a previous protocol optimised for neonatal spatial normalisation, and that TSA projects FA values that match well with values derived from native space tractography. We apply TSA for the first time to a preterm neonatal population to study the effects of age at scan on WM tracts around term equivalent age. We demonstrate the effects of age at scan on DTI metrics in commissural, projection and association fibres. We demonstrate the potential of TSA for WM analysis and its suitability for infant studies involving multiple tracts.

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Evaluation of tract-specific analysis (TSA) for white matter studies in infants.

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TSA improves white matter tract alignment over scalar-based registration.

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TSA closely approximates native space tractography DTI values.

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The first application of TSA to a neonatal population.

Geodesic shape regression with multiple geometries and sparse parameters

Many problems in medicine are inherently dynamic processes which include the aspect of change over time, such as childhood development, aging, and disease progression. From medical images, numerous geometric structures can be extracted with various representations, such as landmarks, point clouds, curves, and surfaces. Different sources of geometry may characterize different aspects of the anatomy, such as fiber tracts from DTI and subcortical shapes from structural MRI, and therefore require a modeling scheme which can include various shape representations in any combination. In this paper, we present a geodesic regression model in the large deformation (LDDMM) framework applicable to multi-object complexes in a variety of shape representations. Our model decouples the deformation parameters from the specific shape representations, allowing the complexity of the model to reflect the nature of the shape changes, rather than the sampling of the data. As a consequence, the sparse representation of diffeomorphic flow allows for the straightforward embedding of a variety of geometry in different combinations, which all contribute towards the estimation of a single deformation of the ambient space. Additionally, the sparse representation along with the geodesic constraint results in a compact statistical model of shape change by a small number of parameters defined by the user. Experimental validation on multi-object complexes demonstrate robust model estimation across a variety of parameter settings. We further demonstrate the utility of our method to support the analysis of derived shape features, such as volume, and explore shape model extrapolation. Our method is freely available in the software package deformetrica which can be downloaded at www.deformetrica.org.

FADTTSter: Accelerating Hypothesis Testing With Functional Analysis of Diffusion Tensor Tract Statistics

Functional Analysis of Diffusion Tensor Tract Statistics (FADTTS) is a toolbox for analysis of white matter (WM) fiber tracts. It allows associating diffusion properties along major WM bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these WM tract properties. However, to use this toolbox, a user must have an intermediate knowledge in scripting languages (MATLAB). FADTTSter was created to overcome this issue and make the statistical analysis accessible to any non-technical researcher. FADTTSter is actively being used by researchers at the University of North Carolina. FADTTSter guides non-technical users through a series of steps including quality control of subjects and fibers in order to setup the necessary parameters to run FADTTS. Additionally, FADTTSter implements interactive charts for FADTTS' outputs. This interactive chart enhances the researcher experience and facilitates the analysis of the results. FADTTSter's motivation is to improve usability and provide a new analysis tool to the community that complements FADTTS. Ultimately, by enabling FADTTS to a broader audience, FADTTSter seeks to accelerate hypothesis testing in neuroimaging studies involving heterogeneous clinical data and diffusion tensor imaging. This work is submitted to the Biomedical Applications in Molecular, Structural, and Functional Imaging conference. The source code of this application is available in NITRC.

UNC-Emory Infant Atlases for Macaque Brain Image Analysis: Postnatal Brain Development through 12 Months

Computational anatomical atlases have shown to be of immense value in neuroimaging as they provide age appropriate reference spaces alongside ancillary anatomical information for automated analysis such as subcortical structural definitions, cortical parcellations or white fiber tract regions. Standard workflows in neuroimaging necessitate such atlases to be appropriately selected for the subject population of interest. This is especially of importance in early postnatal brain development, where rapid changes in brain shape and appearance render neuroimaging workflows sensitive to the appropriate atlas choice. We present here a set of novel computation atlases for structural MRI and Diffusion Tensor Imaging as crucial resource for the analysis of MRI data from non-human primate rhesus monkey (Macaca mulatta) data in early postnatal brain development. Forty socially-housed infant macaques were scanned longitudinally at ages 2 weeks, 3, 6, and 12 months in order to create cross-sectional structural and DTI atlases via unbiased atlas building at each of these ages. Probabilistic spatial prior definitions for the major tissue classes were trained on each atlas with expert manual segmentations. In this article we present the development and use of these atlases with publicly available tools, as well as the atlases themselves, which are publicly disseminated to the scientific community.

Tractography in the clinics: Implementing a pipeline to characterize early brain development

In imaging studies of neonates, particularly in the clinical setting, diffusion tensor imaging-based tractography is typically unreliable due to the use of fast acquisition protocols that yield low resolution and signal-to-noise ratio (SNR). These image acquisition protocols are implemented with the aim of reducing motion artifacts that may be produced by the movement of the neonate's head during the scanning session. Furthermore, axons are not yet fully myelinated in these subjects. As a result, the water molecules' movements are not as constrained as in older brains, making it even harder to define structure using diffusion profiles. Here, we introduce a post-processing method that overcomes the difficulties described above, allowing the determination of reliable tracts in newborns. We tested our method using neonatal data and successfully extracted some of the limbic, association and commissural fibers, all of which are typically difficult to obtain by direct tractography. Geometrical and diffusion based features of the tracts are then utilized to compare premature babies to term babies. Our results quantify the maturation of white matter fiber tracts in neonates.

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The proposed method enables consistent tractography in clinical datasets.

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The tractography is used to structural positioning purposes

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Geometrical features and diffusion variables in the tracts' paths are analyzed.

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The gestational age was predicted with regressions in term and preterm babies.

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The extracted features can be used as indexes of early neurodevelopment.

Common and heritable components of white matter microstructure predict cognitive function at 1 and 2 y

Previous studies indicate that the microstructure of individual white matter (WM) tracts is related to cognitive function. More recent studies indicate that the microstructure of individual tracts is highly correlated and that a property common across WM is related to overall cognitive function in adults. However, little is known about whether these common WM properties exist in early childhood development or how they are related to cognitive development. In this study, we used diffusion tensor imaging (DTI) to investigate common underlying factors in 12 fiber tracts, their relationship with cognitive function, and their heritability in a longitudinal sample of healthy children at birth (n = 535), 1 y (n = 322), and 2 y (n = 244) of age. Our data show that, in neonates, there is a highly significant correlation between major WM tracts that decreases from birth to 2 y of age. Over the same period, the factor structure increases in complexity, from one factor at birth to three factors at age 2 y, which explain 50% of variance. The identified common factors of DTI metrics in each age group are significantly correlated with general cognitive scores and predict cognitive ability in later childhood. These factors are moderately heritable. These findings illustrate the anatomical differentiation of WM fiber from birth to 2 y of age that correlate with cognitive development. Our results also suggest that the common factor approach is an informative way to study WM development and its relationship with cognition and is a useful approach for future imaging genetic studies.

Maturation Along White Matter Tracts in Human Brain Using a Diffusion Tensor Surface Model Tract-Specific Analysis

Previous diffusion tensor imaging tractography studies have demonstrated exponential patterns of developmental changes for diffusion parameters such as fractional anisotropy (FA) and mean diffusivity (MD) averaged over all voxels in major white matter (WM) tracts of the human brain. However, this assumes that the entire tract is changing in unison, which may not be the case. In this study, a surface model based tract-specific analysis was applied to a cross-sectional cohort of 178 healthy subjects (83 males/95 females) aged from 6 to 30 years to spatially characterize the age-related changes of FA and MD along the trajectory of seven major WM tracts - corpus callosum (CC) and six bilateral tracts. There were unique patterns of regions that showed different exponential and linear rates of increasing FA or decreasing MD and age at which FA or MD levels off along each tract. Faster change rate of FA was observed in genu of CC and frontal-parietal part of superior longitudinal fasciculus (SLF). Inferior corticospinal tract (CST), posterior regions of association tracts such as inferior longitudinal fasciculus, inferior frontal occipital fasciculus and uncinate fasciculus also displayed earlier changing patterns for FA. MD decreases with age also exhibited this posterior-to-anterior WM maturation pattern for most tracts in females. Both males and females displayed similar FA/MD patterns of change with age along most large tracts; however, males had overall reached the FA maxima or MD minima later compared with females in most tracts with the greater differences occurring in the CST and frontal-parietal part of SLF for MD. Therefore, brain WM development has spatially varying trajectories along tracts that depend on sex and the tract.

CHIMERA: Clustering of Heterogeneous Disease Effects via Distribution Matching of Imaging Patterns

Many brain disorders and diseases exhibit heterogeneous symptoms and imaging characteristics. This heterogeneity is typically not captured by commonly adopted neuroimaging analyses that seek only a main imaging pattern when two groups need to be differentiated (e.g., patients and controls, or clinical progressors and non-progressors). We propose a novel probabilistic clustering approach, CHIMERA, modeling the pathological process by a combination of multiple regularized transformations from normal/control population to the patient population, thereby seeking to identify multiple imaging patterns that relate to disease effects and to better characterize disease heterogeneity. In our framework, normal and patient populations are considered as point distributions that are matched by a variant of the coherent point drift algorithm. We explain how the posterior probabilities produced during the MAP optimization of CHIMERA can be used for clustering the patients into groups and identifying disease subtypes. CHIMERA was first validated on a synthetic dataset and then on a clinical dataset mixing 317 control subjects and patients suffering from Alzheimer's Disease (AD) and Parkison's Disease (PD). CHIMERA produced better clustering results compared to two standard clustering approaches. We further analyzed 390 T1 MRI scans from Alzheimer's patients. We discovered two main and reproducible AD subtypes displaying significant differences in cognitive performance.

Altered white matter and cortical structure in neonates with antenatally diagnosed isolated ventriculomegaly

Ventriculomegaly (VM) is the most common central nervous system abnormality diagnosed antenatally, and is associated with developmental delay in childhood. We tested the hypothesis that antenatally diagnosed isolated VM represents a biological marker for altered white matter (WM) and cortical grey matter (GM) development in neonates.

25 controls and 21 neonates with antenatally diagnosed isolated VM had magnetic resonance imaging at 41.97(± 2.94) and 45.34(± 2.14) weeks respectively. T₂-weighted scans were segmented for volumetric analyses of the lateral ventricles, WM and cortical GM. Diffusion tensor imaging (DTI) measures were assessed using voxel-wise methods in WM and cortical GM; comparisons were made between cohorts.

Ventricular and cortical GM volumes were increased, and WM relative volume was reduced in the VM group. Regional decreases in fractional anisotropy (FA) and increases in mean diffusivity (MD) were demonstrated in WM of the VM group compared to controls. No differences in cortical DTI metrics were observed. At 2 years, neurodevelopmental delays, especially in language, were observed in 6/12 cases in the VM cohort.

WM alterations in isolated VM cases may be consistent with abnormal development of WM tracts involved in language and cognition. Alterations in WM FA and MD may represent neural correlates for later neurodevelopmental deficits.

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This study compared brain development in neonates with isolated VM to controls.

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Neonates with isolated VM have enlarged cortical volumes compared to controls.

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FA was reduced and MD was increased in the WM of the VM cohort.

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Children with antenatal isolated VM are at increased risk for language delay.

Profilometry: A new statistical framework for the characterization of white matter pathways, with application to multiple sclerosis

AIMS

describe a new "profilometry" framework for the multimetric analysis of white matter tracts, and demonstrate its application to multiple sclerosis (MS) with radial diffusivity (RD) and myelin water fraction (MWF).

METHODS

A cohort of 15 normal controls (NC) and 141 MS patients were imaged with T1, T2 FLAIR, T2 relaxometry and diffusion MRI (dMRI) sequences. T1 and T2 FLAIR allowed for the identification of patients having lesion(s) on the tracts studied, with a special focus on the forceps minor. T2 relaxometry provided MWF maps, while dMRI data yielded RD maps and the tractography required to compute MWF and RD tract profiles. The statistical framework combined a multivariate analysis of covariance (MANCOVA) and a linear discriminant analysis (LDA) both accounting for age and gender, with multiple comparison corrections.

RESULTS

In the single-case case study the profilometry visualization showed a clear departure of MWF and RD from the NC normative data at the lesion location(s). Group comparison from MANCOVA demonstrated significant differences at lesion locations, and a significant age effect in several tracts. The follow-up LDA analysis suggested MWF better discriminates groups than RD.

DISCUSSION AND CONCLUSION

While progress has been made in both tract-profiling and metrics for white matter characterization, no single framework for a joint analysis of multimodality tract profiles accounting for age and gender is known to exist. The profilometry analysis and visualization appears to be a promising method to compare groups using a single score from MANCOVA while assessing the contribution of each metric with LDA.