ORCID Profile
0000-0001-5983-397X
Current Organisations
Charles University, First Faculty of Medicine
,
UQ Queensland Brain Institute
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Sensory Processes, Perception and Performance | Sensory Systems | Psychology | Image Processing | Neurosciences | Computer Perception, Memory and Attention
ANZSRC Socio-Economic Objective (SEO)
Related Links
Publications
The spatiotemporal hemodynamic response function for depth-dependent functional imaging of human cortex
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.NEUROIMAGE.2016.06.019
Abstract: The gray matter of human cortex is characterized by depth-dependent differences in neuronal activity and connections (Shipp, 2007) as well as in the associated vasculature (Duvernoy et al., 1981). The resolution limit of functional magnetic resonance imaging (fMRI) measurements is now below a millimeter, promising the non-invasive measurement of these properties in awake and behaving humans (Muckli et al., 2015 Olman et al., 2012 Ress et al., 2007). To advance this endeavor, we present a detailed spatiotemporal hemodynamic response function (HRF) reconstructed through the use of high-resolution, submillimeter fMRI. We decomposed the HRF into directions tangential and perpendicular to the cortical surface and found that key spatial properties of the HRF change significantly with depth from the cortical surface. Notably, we found that the spatial spread of the HRF increases linearly from 4.8mm at the gray/white matter boundary to 6.6mm near the cortical surface. Using a hemodynamic model, we posit that this effect can be explained by the depth profile of the cortical vasculature, and as such, must be taken into account to properly estimate the underlying neuronal responses at different cortical depths.
Measuring the effects of attention to individual fingertips in somatosensory cortex using ultra-high field (7T) fMRI
Publisher: Elsevier BV
Date: 11-2017
DOI: 10.1016/J.NEUROIMAGE.2017.08.014
Abstract: Attention to sensory information has been shown to modulate the neuronal processing of that information. For ex le, visuospatial attention acts by modulating responses at retinotopically appropriate regions of visual cortex (Puckett and DeYoe, 2015 Tootell et al. 1998). Much less, however, is known about the neuronal processing associated with attending to other modalities of sensory information. One reason for this is that visual cortex is relatively large, and therefore easier to access non-invasively in humans using tools such as functional magnetic resonance imaging (fMRI). With high-resolution fMRI, however, it is now possible to access smaller cortical areas such as primary somatosensory cortex (Martuzzi et al., 2014 Sanchez-Panchuelo et al., 2010 Schweisfurth et al. 2014 Schweizer et al. 2008). Here, we combined a novel experimental design and high-resolution fMRI at ultra-high field (7T) to measure the effects of attention to tactile stimulation in primary somatosensory cortex, S1. We find that attention modulates somatotopically appropriate regions of S1, and importantly, that this modulation can be measured at the level of the cortical representation of in idual fingertips.
Susceptibility artifact correction for sub-millimeter fMRI using inverse phase encoding registration and T1 weighted regularization.
Publisher: Elsevier BV
Date: 04-2020
Variability of visual field maps in human early extrastriate cortex challenges the canonical model of organization of V2 and V3
Publisher: Cold Spring Harbor Laboratory
Date: 18-10-2022
DOI: 10.1101/2022.10.16.511648
Abstract: Visual field maps in human early extrastriate areas (V2 and V3) are traditionally thought to form mirror-image representations which surround the primary visual cortex (V1). According to this scheme, V2 and V3 form nearly symmetrical halves with respect to the calcarine sulcus, with the dorsal halves representing lower contralateral quadrants, and the ventral halves representing upper contralateral quadrants. This arrangement is considered to be consistent across in iduals, and thus predictable with reasonable accuracy using templates. However, data that deviate from this expected pattern have been observed, but mainly treated as artifactual. Here we systematically investigate in idual variability in the visual field maps of human early visual cortex using the 7T Human Connectome Project (HCP) retinotopy dataset. Our results demonstrate substantial and principled inter-in idual variability. Visual field representation in the dorsal portions of V2 and V3 was more variable than in their ventral counterparts, including substantial departures from the expected mirror-symmetrical patterns. In addition, left hemisphere retinotopic maps were more variable than those in the right hemisphere. Surprisingly, only one-third of in iduals had maps that conformed to the expected pattern in the left hemisphere. Visual field sign analysis further revealed that in many in iduals the area conventionally identified as dorsal V3 shows a discontinuity in the mirror-image representation of the retina, associated with a Y-shaped lower vertical representation. Our findings challenge the current view that inter-in idual variability in early extrastriate cortex is negligible, and that the dorsal portions of V2 and V3 are roughly mirror images of their ventral counterparts.
Variability of visual field maps in human early extrastriate cortex challenges the canonical model of organization of V2 and V3
Publisher: eLife Sciences Publications, Ltd
Date: 15-08-2023
DOI: 10.7554/ELIFE.86439
Abstract: Visual field maps in human early extrastriate areas (V2 and V3) are traditionally thought to form mirror-image representations which surround the primary visual cortex (V1). According to this scheme, V2 and V3 form nearly symmetrical halves with respect to the calcarine sulcus, with the dorsal halves representing lower contralateral quadrants, and the ventral halves representing upper contralateral quadrants. This arrangement is considered to be consistent across in iduals, and thus predictable with reasonable accuracy using templates. However, data that deviate from this expected pattern have been observed, but mainly treated as artifactual. Here, we systematically investigate in idual variability in the visual field maps of human early visual cortex using the 7T Human Connectome Project (HCP) retinotopy dataset. Our results demonstrate substantial and principled inter-in idual variability. Visual field representation in the dorsal portions of V2 and V3 was more variable than in their ventral counterparts, including substantial departures from the expected mirror-symmetrical patterns. In addition, left hemisphere retinotopic maps were more variable than those in the right hemisphere. Surprisingly, only one-third of in iduals had maps that conformed to the expected pattern in the left hemisphere. Visual field sign analysis further revealed that in many in iduals the area conventionally identified as dorsal V3 shows a discontinuity in the mirror-image representation of the retina, associated with a Y-shaped lower vertical representation. Our findings challenge the current view that inter-in idual variability in early extrastriate cortex is negligible, and that the dorsal portions of V2 and V3 are roughly mirror images of their ventral counterparts.
Manipulating the structure of natural scenes using wavelets to study the functional architecture of perceptual hierarchies in the brain
Publisher: Elsevier BV
Date: 11-2020
Imaging somatosensory cortex: human functional magnetic resonance imaging (fMRI)
Publisher: Center for Open Science
Date: 20-07-2022
Abstract: Functional magnetic resonance imaging (fMRI) is a powerful tool for imaging somatosensory cortex, providing a means to non-invasively measure cortical activity in awake and behaving humans. Notably, this technique has permitted the homunculus – a hallmark of primary somatosensory cortex (S1) organization – to be examined with unprecedented detail. With the development of high-resolution fMRI (mostly at ultra-high field, 7 Tesla), it is now possible to investigate the finer topographic details of the sensory homunculus in almost any in idual. Moreover, fMRI can be used to investigate other various bottom-up response properties as well as more top-down perceptual and cognitive processes (e.g., attention and prediction) across a wide range of experimental conditions. This chapter mainly focuses on tactile experiments, outlining a number of experimental paradigms and analysis techniques practical and participant-specific difficulties are noted. Although we focus on fMRI for imaging primary somatosensory cortex, this technique can also be used to image cortical activity in other areas involved in somatosensory processing such as secondary somatosensory cortex (S2), insular cortex, or the cerebellum.
Vascular effects on the BOLD response and the retinotopic mapping of hV4
Publisher: Cold Spring Harbor Laboratory
Date: 10-09-2018
DOI: 10.1101/413492
Abstract: Despite general acceptance that the retinotopic organisation of human V4 (hV4) takes the form of a single, uninterrupted ventral hemifield, measured retinotopic maps of this visual area are often incomplete. Here, we test hypotheses that artefact from draining veins close to hV4 cause inverted BOLD responses that may serve to obscure a portion of the lower visual quarterfield — including the lower vertical meridian — in some hemispheres. We further test whether correcting such responses can restore the ‘missing’ retinotopic coverage in hV4. Subjects (N=11) viewed bowtie, ring, drifting bar and full field flash stimuli. Functional EPIs were acquired over approximately 1.5h and analysed to reveal retinotopic maps of early visual cortex, including hV4. Normalised mean maps (which show the average EPI signal litude) were constructed by voxel-wise averaging of the EPI time course and used to locate venous eclipses, which can be identified by a decrease in the EPI signal caused by deoxygenated blood. Inverted responses are shown to cluster in these regions, and correcting these responses improves maps of hV4 in some hemispheres, including restoring a complete hemifield map in one. A leftwards bias was found in which 11/11 hV4 maps in the left hemisphere were classified as incomplete, while this was the case in only 3/11 right hemisphere maps. Incomplete hV4 maps did not correspond with venous artefact in many instances, with incomplete maps being present in the absence of a venous eclipse and complete maps coexisting with a proximate venous eclipse. We also show that mean maps of upper surfaces (near the boundary between cortical grey matter and CSF) provide highly detailed maps of veins on the cortical surface. Results suggest that venous eclipses and inverted voxels can explain some incomplete hV4 maps, but cannot explain the remainder nor the leftwards bias in hV4 coverage reported here.
Cytokine polymorphism in noninfectious uveitis.
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 08-2010
DOI: 10.1167/IOVS.09-4583
Abstract: Noninfectious uveitis is a sight-threatening immune-mediated intraocular inflammatory disorder. The inheritance of uveitis in multiplex families and its association with known monogenic and polygenic immunologic disorders suggests that common genetic variants underlie susceptibility to uveitis as well as to other immunologic disorders. TNFA and IL10 are strong candidate genes, given the influence of these cytokines on inflammation, immune tolerance, and apoptosis. The role of 12 polymorphisms spanning the TNFA and IL10 genomic regions was investigated in 192 uveitis patients and 92 population control subjects from four regional centers in the United Kingdom and Republic of Ireland. The results demonstrate that uveitis is associated with three haplotype-tagging SNPs (htSNPs) in the IL10 gene: htSNP2 (rs6703630), htSNP5 (rs2222202), and htSNP6 (rs3024490). IL10htSNP2AG/htSNP5TC was the most significantly associated haplotype (P = 0.00085), whereas the LTA+252AA/TNFhtSNP2GG haplotype was protective (P = 0.00031). Furthermore, subgroup analysis showed that the frequency of the TNFd4 allele was higher in patients with nonremitting ocular disease and/or those requiring higher levels of maintenance immunosuppression. Although these associations lost significance after Bonferroni correction, they infer a relationship that may be validated by a larger study. Since these variants are implicated in the susceptibility and severity of several immunologic disorders, the results support the hypothesis that common genetic determinants influence shared mechanisms of autoimmunity.
Punctate inner choroidopathy and multifocal choroiditis with panuveitis share haplotypic associations with IL10 and TNF loci.
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 26-05-2011
DOI: 10.1167/IOVS.10-6743
Abstract: The white-dot syndromes are a heterogenous group of chorioretinal disorders that have many common clinical features. Whether these disorders represent distinct clinical entities or different manifestations of the same disease warrants further interrogation. Two white-dot syndromes were investigated, with closely overlapping phenotypes--multifocal choroiditis with panuveitis (MFCPU) and punctate inner choroidopathy (PIC)--for differences in clinical course and genotype frequency at IL10 and TNF loci, known to be associated with noninfectious uveitis. Twelve polymorphisms were genotyped, spanning the TNFA and IL10 genomic regions, in 61 patients with MFCPU or PIC and 92 population controls from the United Kingdom and Republic of Ireland. There were clear differences in clinical course between patients with MFCPU and PIC which had prognostic significance. However, both patient groups demonstrated similar associations with the IL10 haplotype, IL10htSNP2(-2849)AX/htSNP5(+434)TC and negative associations with the TNF haplotype, LTA+252A/TNFhtSNP1(-308)G/TNFhtSNP2(-238)G/TNFhtSNP3(+488)A/TNFd3. Despite clear differences in clinical course and outcome, MFCPU and PIC may still represent two manifestations of the same disease, given their similar genetic associations with IL10 and TNF loci, which are known to be associated with noninfectious uveitis and autoimmunity, in general. Definitive proof will necessitate genomewide sequence analysis. However, the data also support the notion that epigenetic factors have a strong effect on clinical phenotype.
Towards concrete, in-depth and applicable predictions of BOLD responses; modelling the complete cascade from visual stimulus to neuronal response to vascular hemodynamics.
Publisher: Frontiers Media SA
Date: 2013
Using multi-echo simultaneous multi-slice (SMS) EPI to improve functional MRI of the subcortical nuclei of the basal ganglia at ultra-high field (7T)
Publisher: Elsevier BV
Date: 05-2018
DOI: 10.1016/J.NEUROIMAGE.2017.12.005
Abstract: The nuclei of the basal ganglia pose a special problem for functional MRI, especially at ultra-high field, because T2* variations between different regions result in suboptimal BOLD sensitivity when using gradient-echo echo-planar imaging (EPI). Specifically, the iron-rich lentiform nucleus of the basal ganglia, including the putamen and globus pallidus, suffers from substantial signal loss when imaging is performed using conventional single-echo EPI with echo times optimized for the cortex. Multi-echo EPI acquires several echoes at different echo times for every imaging slice, allowing images to be reconstructed with a weighting of echo times that is optimized in idually for each voxel according to the underlying tissue or T2* properties. Here we show that multi-echo simultaneous multi-slice (SMS) EPI can improve functional activation of iron-rich subcortical regions while maintaining sensitivity within cortical areas. Functional imaging during a motor task known to elicit strong activations in the cortex and the subcortex (basal ganglia) was performed to compare the performance of multi-echo SMS EPI to single-echo SMS EPI. Notably within both the caudate nucleus and putamen of the basal ganglia, multi-echo SMS EPI yielded higher tSNR (an average 84% increase) and CNR (an average 58% increase), an approximate 3-fold increase in supra-threshold voxels, and higher t-values (an average 39% increase). The degree of improvement in the group level t-statistics was negatively correlated to the underlying T2* of the voxels, such that the shorter the T2*, as in the iron-rich nuclei of the basal ganglia, the higher the improvement of t-values in the activated region.
Measuring the attentional field throughout human visual cortex
Publisher: Frontiers Media SA
Date: 2013
Vascular effects on the BOLD response and the retinotopic mapping of hV4
Publisher: Public Library of Science (PLoS)
Date: 13-06-2019
Author response: Variability of visual field maps in human early extrastriate cortex challenges the canonical model of organization of V2 and V3
Publisher: eLife Sciences Publications, Ltd
Date: 04-07-2023
Serial correlations in single-subject fMRI with sub-second TR
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.NEUROIMAGE.2017.10.043
Abstract: When performing statistical analysis of single-subject fMRI data, serial correlations need to be taken into account to allow for valid inference. Otherwise, the variability in the parameter estimates might be under-estimated resulting in increased false-positive rates. Serial correlations in fMRI data are commonly characterized in terms of a first-order autoregressive (AR) process and then removed via pre-whitening. The required noise model for the pre-whitening depends on a number of parameters, particularly the repetition time (TR). Here we investigate how the sub-second temporal resolution provided by simultaneous multislice (SMS) imaging changes the noise structure in fMRI time series. We fit a higher-order AR model and then estimate the optimal AR model order for a sequence with a TR of less than 600 ms providing whole brain coverage. We show that physiological noise modelling successfully reduces the required AR model order, but remaining serial correlations necessitate an advanced noise model. We conclude that commonly used noise models, such as the AR(1) model, are inadequate for modelling serial correlations in fMRI using sub-second TRs. Rather, physiological noise modelling in combination with advanced pre-whitening schemes enable valid inference in single-subject analysis using fast fMRI sequences.
Predicting the retinotopic organization of human visual cortex from anatomy using geometric deep learning
Publisher: Cold Spring Harbor Laboratory
Date: 12-02-2020
DOI: 10.1101/2020.02.11.934471
Abstract: Whether it be in a single neuron or a more complex biological system like the human brain, form and function are often directly related. The functional organization of human visual cortex, for instance, is tightly coupled with the underlying anatomy with cortical shape having been shown to be a useful predictor of the retinotopic organization in early visual cortex. Although the current state-of-the-art in predicting retinotopic maps is able to account for gross in idual differences, such models are unable to account for any idiosyncratic differences in the structure-function relationship from anatomical information alone due to their initial assumption of a template. Here we developed a geometric deep learning model capable of exploiting the actual structure of the cortex to learn the complex relationship between brain function and anatomy in human visual cortex such that more realistic and idiosyncratic maps could be predicted. We show that our neural network was not only able to predict the functional organization throughout the visual cortical hierarchy, but that it was also able to predict nuanced variations across in iduals. Although we demonstrate its utility for modeling the relationship between structure and function in human visual cortex, our approach is flexible and well-suited for a range of other applications involving data structured in non-Euclidean spaces.
The Attentional Field Revealed by Single-Voxel Modeling of fMRI Time Courses
Publisher: Society for Neuroscience
Date: 25-03-2015
DOI: 10.1523/JNEUROSCI.3754-14.2015
Abstract: The spatial topography of visual attention is a distinguishing and critical feature of many theoretical models of visuospatial attention. Previous fMRI-based measurements of the topography of attention have typically been too crude to adequately test the predictions of different competing models. This study demonstrates a new technique to make detailed measurements of the topography of visuospatial attention from single-voxel, fMRI time courses. Briefly, this technique involves first estimating a voxel's population receptive field (pRF) and then “drifting” attention through the pRF such that the modulation of the voxel's fMRI time course reflects the spatial topography of attention. The topography of the attentional field (AF) is then estimated using a time-course modeling procedure. Notably, we are able to make these measurements in many visual areas including smaller, higher order areas, thus enabling a more comprehensive comparison of attentional mechanisms throughout the full hierarchy of human visual cortex. Using this technique, we show that the AF scales with eccentricity and varies across visual areas. We also show that voxels in multiple visual areas exhibit suppressive attentional effects that are well modeled by an AF having an enhancing Gaussian center with a suppressive surround. These findings provide extensive, quantitative neurophysiological data for use in modeling the psychological effects of visuospatial attention.
Bayesian population receptive field modeling in human somatosensory cortex
Publisher: Elsevier BV
Date: 03-2020
DOI: 10.1016/J.NEUROIMAGE.2019.116465
Abstract: Somatosensation is fundamental to our ability to sense our body and interact with the world. Our body is continuously s ling the environment using a variety of receptors tuned to different features, and this information is routed up to primary somatosensory cortex. Strikingly, the spatial organization of the peripheral receptors in the body are well maintained, with the resulting representation of the body in the brain being referred to as the somatosensory homunculus. Recent years have seen considerable advancements in the field of high-resolution fMRI, which have enabled an increasingly detailed examination of the organization and properties of this homunculus. Here we combined advanced imaging techniques at ultra-high field (7T) with a recently developed Bayesian population receptive field (pRF) modeling framework to examine pRF properties in primary somatosensory cortex. In each subject, vibrotactile stimulation of the fingertips (i.e., the peripheral mechanoreceptors) modulated the fMRI response along the post-central gyrus and these signals were used to estimate pRFs. We found the pRF center location estimates to be in accord with previous work as well as evidence of other properties in line with the underlying neurobiology. Specifically, as expected from the known properties of cortical magnification, we find a larger representation of the index finger compared to the other stimulated digits (middle, index, little). We also show evidence that the little finger is marked by the largest pRF sizes, and that pRF size increases from anterior to posterior regions of S1. The ability to estimate somatosensory pRFs in humans provides an unprecedented opportunity to examine the neural mechanisms underlying somatosensation and is critical for studying how the brain, body, and environment interact to inform perception and action.
An investigation of positive and inverted hemodynamic response functions across multiple visual areas
Publisher: Wiley
Date: 04-07-2014
DOI: 10.1002/HBM.22569
Bayesian population receptive field modeling in human somatosensory cortex
Publisher: Cold Spring Harbor Laboratory
Date: 16-03-2019
DOI: 10.1101/577981
Abstract: Somatosensation is fundamental to our ability to sense our body and interact with the world. Our body is continuously s ling the environment using a variety of receptors tuned to different features, and this information is routed up to primary somatosensory cortex. Strikingly, the spatial organization of the peripheral receptors in the body are well maintained, with the resulting representation of the body in the brain being referred to as the somatosensory homunculus. Recent years have seen considerable advancements in the field of high-resolution fMRI, which have enabled an increasingly detailed examination of the organization and properties of this homunculus. Here we combined advanced imaging techniques at ultra-high field (7T) with a recently developed Bayesian population receptive field (pRF) modeling framework to examine pRF properties in primary somatosensory cortex. In each subject, vibrotactile stimulation of the fingertips (i.e., the peripheral mechanoreceptors) modulated the fMRI response along the post-central gyrus and these signals were used to estimate pRFs. We found the pRF center location estimates to be in accord with previous work as well as evidence of other properties in line with the underlying neurobiology. Specifically, as expected from the known properties of cortical magnification, we find a larger representation of the index finger compared to the other stimulated digits (middle, index, little). We also show evidence that the little finger is marked by the largest pRF sizes. The ability to estimate somatosensory pRFs in humans provides an unprecedented opportunity to examine the neural mechanisms underlying somatosensation and is critical for studying how the brain, body, and environment interact to inform perception and action.
Related Organisations
Related Funding Activities
Ultra-high Resolution Brain Mapping In The Human Early Visual Cortex, Characterizing Laminar Responses And Small Localized Irregular Voxel Responses.
Start Date: 2014
End Date: 2015
Funder: University of Wollongong
View Funded ActivityCortical Layer Specific Functional Imaging Of The Human Brain
Start Date: 2018
End Date: 2020
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP200103386
Start Date: 2020
End Date: 12-2024
Amount: $512,774.00
Funder: Australian Research Council
View Funded ActivityDiscovery Early Career Researcher Award - Grant ID: DE180100433
Start Date: 2018
End Date: 08-2022
Amount: $365,058.00
Funder: Australian Research Council
View Funded Activity