Robert Elton Smith

Robert Elton Smith
The Florey Institute of Neuroscience and Mental Health · Imaging

B. App. Sci. (App. Phys.), B. Eng. (Elec.), PhD

About

78
Publications
23,647
Reads
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4,681
Citations
Citations since 2016
58 Research Items
4511 Citations
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201620172018201920202021202202004006008001,0001,200
201620172018201920202021202202004006008001,0001,200
Introduction
Development of novel image processing algorithms for neuroscientific analysis of diffusion Magnetic Resonance Imaging data Developer of the MRtrix3 software package: mrtrix.org
Additional affiliations
April 2016 - present
The Florey Institute of Neuroscience and Mental Health
Position
  • Research Officer
April 2013 - April 2016
The Florey Institute of Neuroscience and Mental Health
Position
  • Research Officer
May 2009 - February 2013
The Florey Institute of Neuroscience and Mental Health
Position
  • PhD Student
Education
February 2004 - December 2008
RMIT University
Field of study
  • Applied Physics
February 2004 - December 2008
RMIT University
Field of study
  • Electronic Engineering

Publications

Publications (78)
Article
Full-text available
Being on the bleeding edge of research requires the use of new and regularly updated software. The result is the occasional and inevitable occurrence of bugs. In the following work we present a case study where a feature request introduced a bug in a neuroimaging software package, which had consequences for the quality of results in a published art...
Article
Full-text available
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...
Article
Structural connectomes are increasingly mapped at high spatial resolutions comprising many hundreds-if not thousands-of network nodes. However, high-resolution connectomes are particularly susceptible to image registration misalignment, tractography artifacts, and noise, all of which can lead to reductions in connectome accuracy and test-retest rel...
Preprint
Full-text available
Structural connectomes are increasingly mapped at high spatial resolutions comprising many hundreds—if not thousands—of network nodes. However, high-resolution connectomes are particularly susceptible to image registration misalignment, tractography artifacts, and noise, all of which can lead to reductions in connectome accuracy and test-retest rel...
Conference Paper
Full-text available
While the Fixel-Based Analysis (FBA) framework provides familywise error control across a whole-brain template accounting for the presence of crossing fibres in the white matter, its typical usage fails to correct for multiple hypothesis tests due to the utilisation of multiple quantitative metrics. We demonstrate different methods that can be empl...
Preprint
Full-text available
Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections at macro scale. 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 provid...
Chapter
“Tractography” refers to the process of digitally reconstructing the spatial trajectories of elongated thin structures based on a continuous field of local orientation data; most commonly in reference to white matter axons within the central nervous system based on a diffusion Magnetic Resonance Imaging (MRI) model. This technology provides a uniqu...
Article
Full-text available
The diffusion tensor model for diffusion MRI has been used extensively to study asymmetry in the human brain white matter. However, given the limitations of the tensor model, the nature of any underlying asymmetries remains uncertain, particularly in crossing fibre regions. Here, we provide a more robust characterization of human brain white matter...
Article
Full-text available
The aim of the current study was to longitudinally examine how adrenarcheal hormones influence the development of white matter structure from age 8.5 to 10 years. Participants were 120 children (66 female; mean age 8.45 years at Time 1 and 9.97 years at Time 2) who completed two diffusion-weighted imaging scans 1.5 years apart. Morning saliva sampl...
Conference Paper
Full-text available
Alzheimer’s disease (AD) is characterised by degeneration of specific white matter tracts, however the longitudinal trajectory of tract-specific decline has not yet been well described. In this work, we utilise a longitudinal fixel-based analysis framework to investigate specific fibre tracts that exhibit accelerated decline in AD and mild cognitiv...
Article
Full-text available
Head motion is a major confounding factor in neuroimaging studies. While numerous studies have investigated how motion impacts estimates of functional connectivity, the effects of motion on structural connectivity measured using diffusion MRI have not received the same level of attention, despite the fact that, like functional MRI, diffusion MRI re...
Preprint
Full-text available
Recent developments in semi-global tractogram optimisation algorithms have opened the field of diffusion MRI to the possibility of performing quantitative assessment of structural fibre connectivity. The proper application of these methods in neuroscience research has however been limited by a lack of awareness, understanding, or appreciation for t...
Article
Full-text available
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 cha...
Conference Paper
Full-text available
The brain's white matter undergoes profound changes during early childhood that are believed to underlie the rapid development of cognitive and behavioral skills across this period. Diffusion MRI estimates of axonal density and dispersion of axonal projections have been shown to increase with brain development. Widespread increases in estimated axo...
Conference Paper
Full-text available
The "Anatomically-Constrained Tractography (ACT)" framework enhances the biological accuracy of diffusion MRI streamlines tractography reconstruction, by constraining the propagation and termination of streamlines based on tissue segmentation from a high-resolution, high-contrast anatomical image (e.g. T1-weighted). The tissue segmentation image t...
Preprint
Full-text available
Head motion is a major confounding factor in neuroimaging studies. While numerous studies have investigated how motion impacts estimates of functional connectivity, the effects of motion on structural connectivity measured using diffusion MRI have not received the same level of attention, despite the fact that, like functional MRI, diffusion MRI re...
Article
Full-text available
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...
Preprint
Full-text available
Endpoint-to-endpoint fibre bundle connectivity estimated using spherical deconvolution & streamlines tractography in diffusion MRI may be excessive in the presence of pathologies that involve truncation of axons within the white matter. Here we propose a simple modification to an existing method that directly quantifies and corrects for this over-e...
Preprint
Full-text available
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 cha...
Article
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 developm...
Conference Paper
Full-text available
The Fixel-Based Analysis (FBA) framework enables data-driven statistical inference of effects in diffusion MRI measures that is both sensitive and specific to crossing fibre geometry ("fixel": specific fibre bundle element within a specific voxel). A fundamental building block of this framework is the Connectivity-based Fixel Enhancement (CFE) meth...
Conference Paper
Full-text available
Dravet Syndrome is a devastating form of Epilepsy involving infantile seizures and slowing of development after the first year of life. Unlike conventional brain imaging, which shows little evidence of abnormality in these subjects, advanced diffusion MRI analysis based on Constrained Spherical Deconvolution - possessing both sensitivity and specif...
Conference Paper
Early childhood is a period of profound cognitive maturation believed to be related to changes in white matter. Previous diffusion tensor imaging (DTI) studies have shown how white matter tracts mature throughout the lifespan, though few have focused specifically on early childhood. Furthermore, while lifespan development of fractional anisotropy (...
Conference Paper
Full-text available
Fixel-Based Analysis (FBA) enables robust whole-brain statistical analysis of both microscopic and macroscopic white matter properties that is both sensitive and specific to crossing fibre geometry. Given the influence of macroscopic brain differences in such experiments, interest has been expressed in how best to account for variations in brain vo...
Preprint
Full-text available
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 longitudinal changes in white matter micro- and macro-structure, calculated from individually oriented fiber-bundle populations, termed '...
Article
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...
Conference Paper
Full-text available
Fixel-Based Analysis (FBA) enables data-driven statistical inference on quantitative white matter measures derived from diffusion MRI with both sensitivity and specificity to crossing fibre bundle geometry ("fixel": specific fibre bundle element within a specific voxel). This framework relies on spatial normalisation of participant data to a templa...
Conference Paper
Full-text available
Robust and accurate reconstruction of the macroscopic brain structural connectome from diffusion MRI data requires a large number of image processing and digital reconstruction steps. The complexity of such tasks, and the daunting nature of installing and adequately learning one or more neuroimaging software packages, may limit the uptake of state-...
Article
Full-text available
Recent advances in diffusion MRI tractography permit the generation of dense weighted structural connectomes that offer greater insight into brain organization. However, these efforts are hampered by the lack of consensus on how to extract topological measures from the resulting graphs. Here we evaluate the common practice of removing the graphs’ w...
Preprint
Full-text available
MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualization, 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 developm...
Preprint
Full-text available
Recent advances in diffusion MRI tractography permit the generation of dense weighted structural connectomes that offer greater insight into brain organization. However, these efforts are hampered by the lack of consensus on how to extract topological measures from the resulting graphs. Here we evaluate the common practice of removing the graphs’ w...
Article
Full-text available
Differences in brain networks and underlying white matter abnormalities have been suggested to underlie symptoms of autism spectrum disorder (ASD). However, robustly characterizing microstructural white matter differences has been challenging. In the present study, we applied an analytic technique that calculates structural metrics specific to diff...
Article
White matter fibre development in childhood involves dynamic changes to microstructural organisation driven by increasing axon diameter, density, and myelination. However, there is a lack of longitudinal studies that have quantified advanced diffusion metrics to identify regions of accelerated fibre maturation, particularly across the early puberta...
Conference Paper
Full-text available
This study systematically investigates a fundamental question for tractogram- based connectomics research: for a given resolution of brain parcellation, how many streamlines are required for reproducible connectome construction? We incorporate state-of-the-art tractography techniques with surface parcellation schemes of multiple granularities to in...
Preprint
Full-text available
Purpose: White matter fibre development in childhood involves dynamic changes to microstructural organisation driven by increasing axon diameter, density, and myelination. However, there is a lack of longitudinal studies that have quantified advanced diffusion metrics to identify regions of accelerated fibre maturation, particularly across the earl...
Conference Paper
Full-text available
A growing number of studies have identified that relative early/late onset of puberty can lead to differential patterns of microstructural white matter development. The aim of this study was to investigate the longitudinal development of white matter properties using fixel-based analysis (FBA), a method that estimates the microscopic density and ma...
Conference Paper
Full-text available
Early childhood is a period of profound white matter maturation, as reflected by developmental changes in diffusion-tensor derived metrics such as fractional anisotropy and mean diffusivity. These metrics are non-specific however, and are unreliable in regions of crossing and kissing fibers. Higher-order diffusion models and biologically more relev...
Conference Paper
Full-text available
A requisite step in performing a Fixel-Based Analysis (FBA) is the determination of "fixel correspondence", which defines how discrete fibre elements (fixels) for a particular subject map to the fixels defined in each voxel in template space. The method used thus far for this purpose - simply selecting the subject fixel that best aligns with the te...
Article
Full-text available
Interest in the study of brain connectivity is growing, particularly in understanding the dynamics of the structural/functional connectivity relation. Structural and functional connectivity are most often analysed independently of each other. Track-weighted functional connectivity (TW-FC) was recently proposed as a means to combine structural/funct...
Article
Purpose: To investigate whether diffusion MRI can be used to study cortical segregation based on a contrast related to neurite density, thus providing a complementary tool to myelin-based MRI techniques used for myeloarchitecture. Methods: Several myelin-sensitive MRI methods (e.g., based on T1 , T2 , and T2*) have been proposed to parcellate co...
Conference Paper
Full-text available
Synopsis Rich-club organizations, characterizing the higher-level topology of the brain network, has been commonly identií³ˆed from structural connectomes constructed using DTI based on network degrees. This analysis can however be compromised by the following issues: (i) DTI limitations in resolving crossing-í³ˆbers; and (ii) the original degree...
Conference Paper
Full-text available
Neuroimaging studies assessing white and grey matter are most typically performed as independent analyses. The relationships between white and grey matter abnormalities are therefore poorly understood. We present a novel framework for interrogating relationships between quantitative measures derived from grey matter analysis, and diffusion MRI-base...
Conference Paper
Full-text available
Apparent Fibre Density (AFD) is a measure derived from un-normalised fibre orientation distributions. To make AFD quantitative across subjects, images need to be intensity normalised and bias field corrected. Here we present a fast and robust approach to simultaneous bias field correction and intensity normalisation by exploiting tissue compartment...
Conference Paper
Full-text available
This study introduces a novel diffusion MRI streamlines tractography framework called mesh-based anatomically-constrained tractography (MACT) that incorporates high-resolution surface models of various brain tissues as more accurate anatomical constraints in the fibre-tracking process. By detecting intersections between streamlines and tissue surfa...
Article
Full-text available
The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and d...
Preprint
Full-text available
The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and d...
Article
Full-text available
Voxel-based analysis of diffusion MRI data is increasingly popular. However, most white matter voxels contain contributions from multiple fibre populations (often referred to as crossing fibres), and therefore voxel-averaged quantitative measures (e.g. fractional anisotropy) are not fibre-specific and have poor interpretability. Using higher-order...
Conference Paper
Full-text available
Estimation of an appropriate response function for spherical deconvolution is commonly performed using the image data itself, by the following steps: 1. Use some heuristic process to select a subset of white matter voxels considered to contain a single fibre population. 2. Re-orient the diffusion signal in each voxel so that the estimated fibre ori...
Conference Paper
Full-text available
Diffusion MRI streamlines tractography is the main in vivo technique for inferring structural brain connectivity. Ideally, during structural connectome construction, each streamline should connect exactly 2 brain regions-of-interest (i.e. network nodes); the efficacy of identifying such 'pairwise' connectivity has however been shown to be heavily a...
Conference Paper
Full-text available
This study highlights the issue of using the common strategy for assigning individual streamlines to an atlas-based brain parcellation. This process is non-trivial and can introduce ambiguity into connectome quantification. In many fibre-tracking algorithms, track termination criteria can cause premature termination of streamlines within WM or CSF,...
Article
The human connectome is a topologically complex, spatially embedded network. While its topological properties have been richly characterized, the constraints imposed by its spatial embedding are poorly understood. By applying a novel resampling method to tractography data, we show that the brain's spatial embedding makes a major, but not definitive...
Conference Paper
Full-text available
Diffusion weighted imaging (DWI) acquisitions typically suffer from a lower spatial resolution, compared to their T1 structural counterparts, but provide unique angular information. Researchers and clinical users may often find themselves switching back and forth between the "traditional" directionally-encoded colour (DEC) FA map and a T1 map to na...
Conference Paper
Full-text available
The "traditional" directionally-encoded colour (DEC) FA map is an icon of DTI, but is also affected by its inherent flaws. The first eigenvector is known to be ill-defined in regions of crossing fibres, resulting in misleading specific DEC values as well as "false edges" in the overall map. Additionally, the FA shows naturally low values in these r...
Article
A biological parameter that would be valuable to be able to extract from diffusion MRI data is the local white matter axonal density. Track-density imaging (TDI) has been used as if it could provide such a measure; however, this has been the subject of controversy, primarily due to the fact that track-count quantitation is highly sensitive to track...
Article
Full-text available
In brain regions containing crossing fibre bundles, voxel-average diffusion MRI measures such as Fractional Anisotropy (FA) are difficult to interpret, and lack within-voxel single fibre population specificity. Recent work has focused on the development of more interpretable quantitative measures that can be associated with a specific fibre populat...
Conference Paper
Full-text available
Target Audience: Researchers interested in direct inference of group differences in structural or functional connectivity matrices. Introduction: The structural and functional connectivity of the brain is increasingly being interrogated using the framework of the connectome, where connections between pre-defined regions of grey matter are represent...
Conference Paper
Full-text available
The connectome framework is an increasingly popular method of interrogating functional and structural brain connectivity. In population studies, statistical inference at individual connection level lacks power due to the multiple comparisons problem. The Network­Based Statistic (NBS)(Zalesky 2010) method was introduced to address this issue, utiliz...
Conference Paper
Full-text available
Fixel-based morphometry is a novel method for whole-brain white matter morphometry that gives fibre tract-specific information in voxels with crossing fibres.
Article
Recently several novel image contrasts derived from whole-brain fibre tracking-data (tractograms) have been introduced. The novel contrasts of these track-weighted imaging (TWI) methods may provide important information for clinical neuroscience studies. However, before they can be used reliably to generate quantitative measures, it is important to...