Fernando Calamante's research while affiliated with The University of Sydney and other places

Publications (237)

Chapter
The analysis of diffusion weighted brain magnetic resonance images, including the estimation of fibre orientation distribution (FOD), tractography, and connectomics, is a powerful tool for neuroscience research and clinical applications. However, focal brain pathology and imaging acquisition artifacts affecting white matter tracts may disrupt or co...
Article
Full-text available
The International Society for Magnetic Resonance in Medicine (ISMRM) has undoubtedly played a central role in helping shape our field. In particular, the annual meetings have been an avenue of choice for presenting new MR methods, tools, and applications of aspects of our field that have greatly impacted and transformed how MR is used today, and th...
Article
Full-text available
The International Society for Magnetic Resonance in Medicine (ISMRM) has undoubtedly played a central role in helping shape our field. In particular, the annual meetings have been an avenue of choice for presenting new MR methods, tools, and applications of aspects of our field that have greatly impacted and transformed how MR is used today, and th...
Article
Full-text available
The hippocampus supports multiple cognitive functions including episodic memory. Recent work has highlighted functional differences along the anterior-posterior axis of the human hippocampus, but the neuroanatomical underpinnings of these differences remain unclear. We leveraged track-density imaging to systematically examine anatomical connectivit...
Article
Purpose: Brain templates provide an essential standard space for statistical analysis of brain structure and function. Despite recent advances, diffusion MRI still lacks a template of fiber orientation distribution (FOD) and tractography that is unbiased for both white and gray matter. Therefore, we aim to build up a set of such templates for bett...
Preprint
Background. In older people with Mild Cognitive Impairment (MCI), the relationship between early changes in functional connectivity and in vivo changes in key neurometabolites is not known. Two established correlates of MCI diagnosis are decreased in N-Acetylaspartate (NAA) in the hippocampus, indicative of decreased neuronal integrity, and changes...
Article
Full-text available
Purpose: Characterization of cerebral cortex is challenged by the complexity and heterogeneity of its cyto- and myeloarchitecture. This study evaluates quantitative MRI metrics, measured across two cortical depths and in subcortical white matter (WM) adjacent to cortex (juxtacortical WM), indicative of myelin content, neurite density, and diffusio...
Preprint
A characteristic feature of human cognition is our ability to 'multi-task' - performing two or more tasks in parallel - particularly when one task is well-learned. How the brain supports this capacity remains poorly understood. Most past studies have focussed on identifying the areas of the brain - typically the dorsolateral prefrontal cortex - tha...
Article
Complex cognitive abilities are thought to arise from the ability of the brain to adaptively reconfigure its internal network structure as a function of task demands. Recent work has suggested that this inherent flexibility may in part be conferred by the widespread projections of the ascending arousal systems. While the different components of the...
Article
Mapping the human connectome using fiber-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinica...
Preprint
Full-text available
Federated learning (FL) has been widely employed for medical image analysis to facilitate multi-client collaborative learning without sharing raw data. Despite great success, FL's performance is limited for multiple sclerosis (MS) lesion segmentation tasks, due to variance in lesion characteristics imparted by different scanners and acquisition par...
Article
Structural and functional brain networks are modular. Canonical functional systems, such as the default mode network, are well-known modules of the human brain and have been implicated in a large number of cognitive, behavioral and clinical processes. However, modules delineated in structural brain networks inferred from tractography generally do n...
Article
Full-text available
Background Advancements in hybrid positron emission tomography-magnetic resonance (PET-MR) systems allow for combining the advantages of each modality. Integrating information from MRI and PET can be valuable for diagnosing and treating neurological disorders. However, combining diffusion MRI (dMRI) and PET data, which provide highly complementary...
Preprint
A brain template provides a standard space for statistical analysis of brain structure and function. For decades, the T1- and T2-weighted brain templates have been widely used for brain grey matter anatomical and functional analysis. However, T1- and T2-weighted templates provide very limited information about the axonal organization within the whi...
Preprint
Full-text available
Approximately 65% of moderate to severe traumatic brain injury (msTBI) patients present with poor long-term behavioural outcomes, which can significantly impair activities of daily living. Numerous diffusion-weighted MRI studies have linked these poor outcomes to decreased white matter integrity of several commissural tracts, association fibres and...
Article
Introduction La maladie de Parkinson est habituellement détectée par un examen clinique spécialisé avec de bonnes performances diagnostiques. Néanmoins le diagnostic de la maladie à un stade précoce avec des signes moteurs débutants peut être difficile. Des analyses morphométriques des IRM pondérées T1 ont été proposé pour le diagnostic différentie...
Preprint
Full-text available
Structural and functional brain networks are modular. Canonical functional systems, such as the default mode network, are well-known modules of the human brain and have been implicated in a large number of cognitive, behavioral and clinical processes. However, modules delineated in structural brain networks inferred from tractography generally do n...
Article
Background and aims Diffusion-weighted imaging has been used to quantify peripheral nerve properties; however, traditional post-processing techniques have several limitations. Advanced neuroimaging techniques, which overcome many of these limitations, have not been applied to peripheral nerves. Here, we use state-of-the-art diffusion analysis tools...
Preprint
Full-text available
The hippocampus supports multiple cognitive functions including episodic memory. Recent work has highlighted functional differences along the anterior-posterior axis of the human hippocampus but the neuroanatomical underpinnings of these differences remain unclear. We leveraged track-density imaging to systematically examine anatomical connectivity...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Article
Background and Purpose Recent studies using automated perfusion imaging software have identified adults most likely to benefit from reperfusion therapies in extended time windows. The time course of penumbral tissue is poorly characterized in childhood arterial ischemic stroke (AIS). We explore the feasibility of using automated perfusion-diffusion...
Conference Paper
Objectives Neurodegeneration in ALS follows a diffuse pattern of cortical involvement.¹ We have previously highlighted that thalamic abnormality is a robust disease signature in ALS,² but the integrity of thalamic nuclei and their clinical association remains unclear. We employed a novel segmentation technique for thalamic nuclei and track-weighted...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Article
Social anxiety disorder (SAD) is one of the most common mental health disorders in youth, defined by a persistent and intense fear of negative evaluation by others. Recent research has examined its neurological underpinnings, including structural connectivity changes in the brain. This has been examined through measurement of the white matter (WM)...
Article
Full-text available
The heterogeneity of schizophrenia has defied efforts to derive reproducible and definitive anatomical maps of structural brain changes associated with the disorder. We aimed to map deviations from normative ranges of brain structure for individual patients and evaluate whether the loci of individual deviations recapitulated group-average brain map...
Article
Full-text available
Diffusion MRI (dMRI) tractography is currently the only imaging technique that allows for non-invasive delineation and visualisation of white matter (WM) tracts in vivo prompting rapid advances in related fields of brain MRI research in recent years. One of its major clinical applications is for pre-surgery planning and intraoperative image guidanc...
Article
Full-text available
Objective To implement an advanced spatial penalty-based reconstruction to constrain the intravoxel incoherent motion (IVIM)–diffusion kurtosis imaging (DKI) model and investigate whether it provides a suitable alternative at 1.5 T to the traditional IVIM–DKI model at 3 T for clinical characterization of prostate cancer (PCa) and benign prostatic h...
Article
Full-text available
Deep learning-based convolutional neural networks have recently proved their efficiency in providing fast segmentation of major brain fascicles structures, based on diffusion-weighted imaging. The quantitative analysis of brain fascicles then relies on metrics either coming from the tractography process itself or from each voxel along the bundle. S...
Preprint
Full-text available
Mapping the human connectome using fibre-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinica...
Article
Study objectives: Growing evidence demonstrates pronounced alterations in rest-activity functioning in older adults at-risk for dementia. White matter degeneration, poor cardiometabolic functioning and depression have also been linked to greater risk of decline, however limited studies have examined white matter in relation to rest-activity functi...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Conference Paper
Full-text available
Synopsis We employ structural and di usion MRI metrics to evaluate their e ectiveness for cortical segregation based on myelination, neurite density and microstructure in cortex. Three cortical measures (T1w/T2w, FA and total apparent bre density, AFD , demonstrated signi cant inter-correlations. Two track-weighted parameters (FOD and FA, measured...
Preprint
Full-text available
We introduce a connectomics metric that integrates information on structural connectivity (SC) from diffusion MRI tractography and functional connectivity (FC) from resting-state functional MRI, at individual subject level. The metric is based on the ability of SC to broadly predict FC using a simple linear predictive model; for each connection in...
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...
Preprint
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Preprint
Full-text available
Deep learning-based convolutional neural networks have recently proved their efficiency in providing fast segmentation of major brain fascicles structures, based on diffusion-weighted imaging. The quantitative analysis of brain fascicles then relies on metrics either coming from the tractography process itself or from each voxel along the bundle. S...
Preprint
Full-text available
Background The heterogeneity of schizophrenia has defied efforts to derive reproducible and definitive anatomical maps of structural brain changes associated with the disorder. We aimed to map deviations from normative ranges of brain structure for individual patients and evaluate whether the loci of individual deviations recapitulated group-averag...
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...
Article
Objective Cerebral blood flow (CBF) quantification using dynamic-susceptibility contrast MRI can be achieved via model-independent deconvolution, with local arterial input function (AIF) deconvolution methods identifying multiple arterial regions with unique corresponding arterial input functions. The clinical application of local AIF methods neces...
Article
Full-text available
There is great interest in the study of brain structural connectivity, as white matter abnormalities have been implicated in many disease states. Diffusion magnetic resonance imaging (MRI) provides a powerful means to characterise structural connectivity non-invasively, by using a fibre-tracking algorithm. The most widely used fibre-tracking strate...
Article
Full-text available
Objective To investigate the effect of number and combination of b values used on the accuracy of estimated Intravoxel Incoherent Motion (IVIM) parameters using simulation and clinical data. Materials and methods Simulations with seven combinations of b values were performed for 4, 6, 8, and 13 numbers of b values with six different values of D, D...
Article
Background Arterial spin labeling (ASL) is an emerging MRI technique for noninvasive measurement of cerebral blood flow (CBF) that has been used to show hemodynamic changes in the brains of people with Alzheimer's disease (AD). CBF changes have been measured using positron emission tomography (PET) across the AD spectrum, but ASL showed limited suc...
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...
Article
Full-text available
Brain network modularity analysis has attracted increasing interest due to its capability in measuring the level of integration and segregation across subnetworks. Most studies have focused on extracting modules at a single level, although brain network modules are known to be organized in a hierarchical manner. A few techniques have been developed...
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...
Article
Background and Objectives: Recent studies have used automated perfusion imaging software to identify adults most likely to benefit from reperfusion therapies in extended time windows. The time course of penumbral evolution in childhood arterial ischemic stroke (AIS) is poorly characterised. We investigated the utility of automated perfusion imaging...
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
The human brain is a complex network, in which some brain regions, denoted as 'hub' regions, play critically important roles. Some of these hubs are highly interconnected forming a rich-club organization, which has been identified based on the degree metric from structural connectomes constructed using diffusion tensor imaging (DTI)-based fiber tra...
Article
Full-text available
Schizophrenia is associated with cortical thickness (CT) deficits and breakdown in white matter microstructure. Whether these pathological processes are related remains unclear. We used multimodal neuroimaging to investigate the relationship between regional cortical thinning and breakdown in adjacent infracortical white matter as a function of age...
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...
Article
Full-text available
The conventional way to estimate functional networks is primarily based on Pearson correlation along with classic Fisher Z test. In general, networks are usually calculated at the individual-level and subsequently aggregated to obtain group-level networks. However, such estimated networks are inevitably affected by the inherent large inter-subject...
Article
Full-text available
Background Schizophrenia is associated with cortical thinning and breakdown in white matter microstructure. Whether these pathological processes are related remains unclear. We used multimodal neuroimaging to investigate the relation between regional cortical thinning and breakdown in adjacent infracortical white matter as a function of age and ill...
Article
Full-text available
Background and purpose: Intracranial dural arteriovenous fistulas carry a risk of substantial neurologic complications but can be difficult to detect on structural MR imaging and TOF-MRA. The purpose of this study was to assess the accuracy and added value of 3D pseudocontinuous arterial spin-labeling MR imaging for the detection of these lesions....
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
Full-text available
Cerebellar involvement in cognition, as well as in sensorimotor control, is increasingly recognized and is thought to depend on connections with the cerebral cortex. Anatomical investigations in animals and post-mortem humans have established that cerebro-cerebellar connections are contralateral to each other and include the cerebello-thalamo-corti...
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...
Article
Emerging evidence has linked MRI signal changes in deep nuclei of the brain with repeated administration of gadolinium-based contrast agents. Gadolinium deposits have been confirmed in brain tissue, most notably in the dentate nuclei and globus pallidus. Although some linear contrast agents appear to cause greater MRI signal changes than some macro...