Mark Schira | University of Wollongong (original) (raw)
Papers by Mark Schira
Journal of Vision
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Journal of Vision
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Journal of Vision
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Journal of Vision
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Cannabis and cannabinoid research, 2018
Chronic cannabis use is associated with neuroanatomical alterations in the hippocampus. While adv... more Chronic cannabis use is associated with neuroanatomical alterations in the hippocampus. While adverse impacts of cannabis use are generally attributed to Δ-tetrahydrocannabinol, emerging naturalistic evidence suggests cannabidiol (CBD) is neuroprotective and may ameliorate brain harms associated with cannabis use, including protection from hippocampal volume loss. This study examined whether prolonged administration of CBD to regular cannabis users within the community could reverse or reduce the characteristic hippocampal harms associated with chronic cannabis use. Eighteen regular cannabis users participated in an ∼10-week open-label pragmatic trial involving daily oral administration of 200 mg CBD, with no change to their ongoing cannabis use requested. Participants were assessed at baseline and post-CBD treatment using structural magnetic resonance imaging. Automated longitudinal hippocampal segmentation was performed to assess volumetric change over the whole hippocampus and wi...
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Cognitive, affective & behavioral neuroscience, Jan 8, 2018
Alcohol intoxication is implicated in approximately half of all violent crimes. Over the past sev... more Alcohol intoxication is implicated in approximately half of all violent crimes. Over the past several decades, numerous theories have been proposed to account for the influence of alcohol on aggression. Nearly all of these theories imply that altered functioning in the prefrontal cortex is a proximal cause. In the present functional magnetic resonance imaging (fMRI) experiment, 50 healthy young men consumed either a low dose of alcohol or a placebo and completed an aggression paradigm against provocative and nonprovocative opponents. Provocation did not affect neural responses. However, relative to sober participants, during acts of aggression, intoxicated participants showed decreased activity in the prefrontal cortex, caudate, and ventral striatum, but heightened activation in the hippocampus. Among intoxicated participants, but not among sober participants, aggressive behavior was positively correlated with activation in the medial and dorsolateral prefrontal cortex. These result...
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Natural scenes share a consistent distribution of energy across spatial frequencies (SF) known as... more Natural scenes share a consistent distribution of energy across spatial frequencies (SF) known as the 1/f α amplitude spectrum (α≈0.8–1.5, mean 1.2). This distribution is scale-invariant, which is a fractal characteristic of natural scenes with statistically similar structure at different spatial scales. While the sensitivity of the visual system to the 1/f properties of natural scenes has been studied extensively using psychophysics, relatively little is known about the tuning of cortical responses to these properties. Here, we use fMRI and retinotopic mapping techniques to measure and analyze BOLD responses in early visual cortex (V1, V2, and V3) to synthetic noise images that vary in their 1/f α amplitude spectra (α=0.25 to 2.25, step size: 0.50) and contrast levels (10% and 30%) (Experiment 1). To compare the dependence of the BOLD response between the photometric (intensity based) and geometric (fractal) properties of our stimuli, in Experiment 2 we compared grayscale noise images to their binary (thresholded) counterparts, which contain only black and white regions. In both experiments, early visual cortex responded maximally to stimuli generated to have an input 1/f slope corresponding to natural 1/f α amplitude spectra, and lower BOLD responses were found for steeper or shallower 1/f slopes (peak modulation: 0.59% for 1.25 vs. 0.31% for 2.25). To control for changing receptive field sizes, responses were also analyzed across multiple eccentricity bands in cortical surface space. For most eccentricity bands, BOLD responses were maximal for natural 1/f α amplitude spectra, but importantly there was no difference in the BOLD response to grayscale stimuli and their corresponding thresholded counterparts. Since the thresholding of an image changes its measured 1/f slope (α) but not its fractal characteristics, this suggests that neuronal responses in early visual cortex are not strictly driven by spectral slope values (photometric properties) but rather their embedded geometric, fractal-like scaling properties.
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NeuroImage, 2016
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Experimental Brain Research, Dec 1, 2001
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Journal of Visualized Experiments, 2015
The human hippocampus has been broadly studied in the context of memory and normal brain function... more The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (>3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice's kappa metric. Mean Dice's kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.
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Journal of Vision, 2015
Functional magnetic resonance imaging (fMRI) has become a standard tool in vision science, and so... more Functional magnetic resonance imaging (fMRI) has become a standard tool in vision science, and some properties of visual cortex are fairly well understood and modelled, such as retinotopic organisation, contrast response functions and the spatiotemporal Hemodynamic Response Function (stHRF). Here we combine these individual models into a new framework, integrating existing models. The key components are (i) retinal processing; (ii) accurate retino cortical projection (Schira et al 2010); (iii) neural responses; and a (iv) spatiotemporal hemodynamic modeling (Aquino et al. 2012 PLoS CB), combined to a modular toolbox. We argue that the result is greater than the sum of its parts, allowing the complete simulation of fMRI experiments, from visual input (video) to BOLD responses in space and time on an average cortical surface (FS_average) within a few minutes. This supports a number of novel applications. Firstly, exploring interactions between the models and generating exact predictions for a more realistic testing of each of the integrated models. Secondly, a more precise planning of fMRI experiments by generating concrete hypothesis in the space that is actually measured, such as estimating the effect of spatial and temporal interactions between multiple stimulus components. Thirdly, it provides a novel teaching tool, with approximately 5-10 minutes from stimulus video to simulated BOLD responses on a normal desktop computer. Meeting abstract presented at VSS 2015.
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PsycEXTRA Dataset, 2014
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Frontiers in Psychology, 2015
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Social Neuroscience, 2013
Research with violent offenders and delinquent adolescents suggests that endogenous testosterone ... more Research with violent offenders and delinquent adolescents suggests that endogenous testosterone concentrations have the strongest positive correlations with violence among men who have low concentrations of cortisol. The present study tested the hypothesis that testosterone and cortisol would similarly interact to determine neural activation in regions supporting self-regulation in response to anger provocation. Nineteen healthy Asian male participants were insulted and asked to control their anger during functional magnetic resonance imaging (fMRI). When cortisol levels were low, testosterone positively correlated with activation in the dorsolateral prefrontal cortex (dlPFC) and thalamus, but not when cortisol levels were high. During induced anger control, functional connectivity was increased between the amygdala and a top-down prefrontal cortical control network. Moreover, the amygdala-PFC connectivity was strongest among those high in testosterone and low in cortisol. This research highlights a possible neural mechanism by which testosterone and cortisol may influence anger control.
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NeuroImage, 2014
The cerebellum has classically been linked to motor learning and coordination. However, there is ... more The cerebellum has classically been linked to motor learning and coordination. However, there is renewed interest in the role of the cerebellum in non-motor functions such as cognition and in the context of different neuropsychiatric disorders. The contribution of neuroimaging studies to advancing understanding of cerebellar structure and function has been limited, partly due to the cerebellum being understudied as a result of contrast and resolution limitations of standard structural magnetic resonance images (MRI). These limitations inhibit proper visualization of the highly compact and detailed cerebellar foliations. In addition, there is a lack of robust algorithms that automatically and reliably identify the cerebellum and its subregions, further complicating the design of large-scale studies of the cerebellum. As such, automated segmentation of the cerebellar lobules would allow detailed population studies of the cerebellum and its subregions. In this manuscript, we describe a novel set of high-resolution in vivo atlases of the cerebellum developed by pairing MR imaging with a carefully validated manual segmentation protocol. Using these cerebellar atlases as inputs, we validate a novel automated segmentation algorithm that takes advantage of the neuroanatomical variability that exists in a given population under study in order to automatically identify the cerebellum, and its lobules. Our automatic segmentation results demonstrate good accuracy in the identification of all lobules (mean Kappa [κ]=0.731; range 0.40-0.89), and the entire cerebellum (mean κ=0.925; range 0.90-0.94) when compared to "gold-standard" manual segmentations. These results compare favorably in comparison to other publically available methods for automatic segmentation of the cerebellum. The completed cerebellar atlases are available freely online (http://imaging-genetics.camh.ca/cerebellum) and can be customized to the unique neuroanatomy of different subjects using the proposed segmentation pipeline (https://github.com/pipitone/MAGeTbrain).
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NeuroImage, 2014
Functional magnetic resonance imaging (fMRI) is a powerful and broadly used means of non-invasive... more Functional magnetic resonance imaging (fMRI) is a powerful and broadly used means of non-invasively mapping human brain activity. However fMRI is an indirect measure that rests upon a mapping from neuronal activity to the blood oxygen level dependent (BOLD) signal via hemodynamic effects. The quality of estimated neuronal activity hinges on the validity of the hemodynamic model employed. Recent work has demonstrated that the hemodynamic response has non-separable spatiotemporal dynamics, a key property that is not implemented in existing fMRI analysis frameworks. Here both simulated and empirical data are used to demonstrate that using a physiologically based model of the spatiotemporal hemodynamic response function (stHRF) results in a quantitative improvement of the estimated neuronal response relative to unphysical space-time separable forms. To achieve this, an integrated spatial and temporal deconvolution is established using a recently developed stHRF. Simulated data allows the variation of key parameters such as noise and the spatial complexity of the neuronal drive, while knowing the neuronal input. The results demonstrate that the use of a spatiotemporally integrated HRF can avoid "ghost" neuronal responses that can otherwise be falsely inferred. Applying the spatiotemporal deconvolution to high resolution fMRI data allows the recovery of neuronal responses that are consistent with independent electrophysiological measures.
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NeuroImage, 2013
The hippocampus is a neuroanatomical structure that has been widely studied in the context of lea... more The hippocampus is a neuroanatomical structure that has been widely studied in the context of learning, memory, stress, and neurodegeneration. Neuroanatomically, the hippocampus is subdivided into several subfields with intricate morphologies and complex three-dimensional relationships. Recent studies have demonstrated that the identification of different subfields is possible with high-resolution and -contrast image volumes acquired using ex vivo specimens in a small bore 9.4 T scanner and, more recently, in vivo, at 7 T. In these studies, the neuroanatomical definitions of boundaries between subfields are based upon salient differences in image contrast. Typically, the definition of subfields has not been possible using commonly available magnetic resonance (MR) scanners (i.e.: 1.5 or 3T) due to resolution and contrast limitations. To overcome the limited availability of post-mortem specimens and expertise in state-of-the-art high-field imaging, we propose a coupling of MR acquisition and detailed segmentation techniques that allow for the reliable identification of hippocampal anatomy (including subfields). High-resolution and -contrast T1- and T2-weighted image volumes were acquired from 5 volunteers (2 male; 3 female; age range: 29-57, avg. 37) using a clinical research-grade 3T scanner and have final super-sampled isotropic voxel dimensions of 0.3mm. We demonstrate that by using these acquisition techniques, our data results in contrast-to-noise ratios that compare well with high-resolution images acquired with long scan times using post-mortem data at higher field strengths. For the subfields, the cornus ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, stratum radiatum/stratum lacunosum/stratum moleculare, and subiculum were all labeled as separate structures. Hippocampal volumes are reported for each of the substructures and the hippocampus as a whole (range for hippocampus: 2456.72-3325.02 mm(3)). Intra-rater reliability of our manual segmentation protocol demonstrates high reliability for the whole hippocampus (mean Dice Kappa of 0.91; range 0.90-0.92) and for each of the subfields (range of Dice Kappas: 0.64-0.83). We demonstrate that our reliability is better than the Dice Kappas produced by simulating the following errors: a translation by a single voxel in all cardinal directions and 1% volumetric shrinkage and expansion. The completed hippocampal atlases are available freely online (info2.camh.net/kf-tigr/index.php/Hippocampus) and can be coupled with novel computational neuroanatomy techniques that will allow for them to be customized to the unique neuroanatomy of different subjects, and ultimately be utilized in different analysis pipelines.
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Journal of Vision, 2012
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Journal of Cognitive Neuroscience, 2014
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Journal of Vision
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Journal of Vision
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Journal of Vision
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Journal of Vision
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Cannabis and cannabinoid research, 2018
Chronic cannabis use is associated with neuroanatomical alterations in the hippocampus. While adv... more Chronic cannabis use is associated with neuroanatomical alterations in the hippocampus. While adverse impacts of cannabis use are generally attributed to Δ-tetrahydrocannabinol, emerging naturalistic evidence suggests cannabidiol (CBD) is neuroprotective and may ameliorate brain harms associated with cannabis use, including protection from hippocampal volume loss. This study examined whether prolonged administration of CBD to regular cannabis users within the community could reverse or reduce the characteristic hippocampal harms associated with chronic cannabis use. Eighteen regular cannabis users participated in an ∼10-week open-label pragmatic trial involving daily oral administration of 200 mg CBD, with no change to their ongoing cannabis use requested. Participants were assessed at baseline and post-CBD treatment using structural magnetic resonance imaging. Automated longitudinal hippocampal segmentation was performed to assess volumetric change over the whole hippocampus and wi...
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Cognitive, affective & behavioral neuroscience, Jan 8, 2018
Alcohol intoxication is implicated in approximately half of all violent crimes. Over the past sev... more Alcohol intoxication is implicated in approximately half of all violent crimes. Over the past several decades, numerous theories have been proposed to account for the influence of alcohol on aggression. Nearly all of these theories imply that altered functioning in the prefrontal cortex is a proximal cause. In the present functional magnetic resonance imaging (fMRI) experiment, 50 healthy young men consumed either a low dose of alcohol or a placebo and completed an aggression paradigm against provocative and nonprovocative opponents. Provocation did not affect neural responses. However, relative to sober participants, during acts of aggression, intoxicated participants showed decreased activity in the prefrontal cortex, caudate, and ventral striatum, but heightened activation in the hippocampus. Among intoxicated participants, but not among sober participants, aggressive behavior was positively correlated with activation in the medial and dorsolateral prefrontal cortex. These result...
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Natural scenes share a consistent distribution of energy across spatial frequencies (SF) known as... more Natural scenes share a consistent distribution of energy across spatial frequencies (SF) known as the 1/f α amplitude spectrum (α≈0.8–1.5, mean 1.2). This distribution is scale-invariant, which is a fractal characteristic of natural scenes with statistically similar structure at different spatial scales. While the sensitivity of the visual system to the 1/f properties of natural scenes has been studied extensively using psychophysics, relatively little is known about the tuning of cortical responses to these properties. Here, we use fMRI and retinotopic mapping techniques to measure and analyze BOLD responses in early visual cortex (V1, V2, and V3) to synthetic noise images that vary in their 1/f α amplitude spectra (α=0.25 to 2.25, step size: 0.50) and contrast levels (10% and 30%) (Experiment 1). To compare the dependence of the BOLD response between the photometric (intensity based) and geometric (fractal) properties of our stimuli, in Experiment 2 we compared grayscale noise images to their binary (thresholded) counterparts, which contain only black and white regions. In both experiments, early visual cortex responded maximally to stimuli generated to have an input 1/f slope corresponding to natural 1/f α amplitude spectra, and lower BOLD responses were found for steeper or shallower 1/f slopes (peak modulation: 0.59% for 1.25 vs. 0.31% for 2.25). To control for changing receptive field sizes, responses were also analyzed across multiple eccentricity bands in cortical surface space. For most eccentricity bands, BOLD responses were maximal for natural 1/f α amplitude spectra, but importantly there was no difference in the BOLD response to grayscale stimuli and their corresponding thresholded counterparts. Since the thresholding of an image changes its measured 1/f slope (α) but not its fractal characteristics, this suggests that neuronal responses in early visual cortex are not strictly driven by spectral slope values (photometric properties) but rather their embedded geometric, fractal-like scaling properties.
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NeuroImage, 2016
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Experimental Brain Research, Dec 1, 2001
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Journal of Visualized Experiments, 2015
The human hippocampus has been broadly studied in the context of memory and normal brain function... more The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (>3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice's kappa metric. Mean Dice's kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.
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Journal of Vision, 2015
Functional magnetic resonance imaging (fMRI) has become a standard tool in vision science, and so... more Functional magnetic resonance imaging (fMRI) has become a standard tool in vision science, and some properties of visual cortex are fairly well understood and modelled, such as retinotopic organisation, contrast response functions and the spatiotemporal Hemodynamic Response Function (stHRF). Here we combine these individual models into a new framework, integrating existing models. The key components are (i) retinal processing; (ii) accurate retino cortical projection (Schira et al 2010); (iii) neural responses; and a (iv) spatiotemporal hemodynamic modeling (Aquino et al. 2012 PLoS CB), combined to a modular toolbox. We argue that the result is greater than the sum of its parts, allowing the complete simulation of fMRI experiments, from visual input (video) to BOLD responses in space and time on an average cortical surface (FS_average) within a few minutes. This supports a number of novel applications. Firstly, exploring interactions between the models and generating exact predictions for a more realistic testing of each of the integrated models. Secondly, a more precise planning of fMRI experiments by generating concrete hypothesis in the space that is actually measured, such as estimating the effect of spatial and temporal interactions between multiple stimulus components. Thirdly, it provides a novel teaching tool, with approximately 5-10 minutes from stimulus video to simulated BOLD responses on a normal desktop computer. Meeting abstract presented at VSS 2015.
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PsycEXTRA Dataset, 2014
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Frontiers in Psychology, 2015
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Social Neuroscience, 2013
Research with violent offenders and delinquent adolescents suggests that endogenous testosterone ... more Research with violent offenders and delinquent adolescents suggests that endogenous testosterone concentrations have the strongest positive correlations with violence among men who have low concentrations of cortisol. The present study tested the hypothesis that testosterone and cortisol would similarly interact to determine neural activation in regions supporting self-regulation in response to anger provocation. Nineteen healthy Asian male participants were insulted and asked to control their anger during functional magnetic resonance imaging (fMRI). When cortisol levels were low, testosterone positively correlated with activation in the dorsolateral prefrontal cortex (dlPFC) and thalamus, but not when cortisol levels were high. During induced anger control, functional connectivity was increased between the amygdala and a top-down prefrontal cortical control network. Moreover, the amygdala-PFC connectivity was strongest among those high in testosterone and low in cortisol. This research highlights a possible neural mechanism by which testosterone and cortisol may influence anger control.
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NeuroImage, 2014
The cerebellum has classically been linked to motor learning and coordination. However, there is ... more The cerebellum has classically been linked to motor learning and coordination. However, there is renewed interest in the role of the cerebellum in non-motor functions such as cognition and in the context of different neuropsychiatric disorders. The contribution of neuroimaging studies to advancing understanding of cerebellar structure and function has been limited, partly due to the cerebellum being understudied as a result of contrast and resolution limitations of standard structural magnetic resonance images (MRI). These limitations inhibit proper visualization of the highly compact and detailed cerebellar foliations. In addition, there is a lack of robust algorithms that automatically and reliably identify the cerebellum and its subregions, further complicating the design of large-scale studies of the cerebellum. As such, automated segmentation of the cerebellar lobules would allow detailed population studies of the cerebellum and its subregions. In this manuscript, we describe a novel set of high-resolution in vivo atlases of the cerebellum developed by pairing MR imaging with a carefully validated manual segmentation protocol. Using these cerebellar atlases as inputs, we validate a novel automated segmentation algorithm that takes advantage of the neuroanatomical variability that exists in a given population under study in order to automatically identify the cerebellum, and its lobules. Our automatic segmentation results demonstrate good accuracy in the identification of all lobules (mean Kappa [κ]=0.731; range 0.40-0.89), and the entire cerebellum (mean κ=0.925; range 0.90-0.94) when compared to "gold-standard" manual segmentations. These results compare favorably in comparison to other publically available methods for automatic segmentation of the cerebellum. The completed cerebellar atlases are available freely online (http://imaging-genetics.camh.ca/cerebellum) and can be customized to the unique neuroanatomy of different subjects using the proposed segmentation pipeline (https://github.com/pipitone/MAGeTbrain).
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NeuroImage, 2014
Functional magnetic resonance imaging (fMRI) is a powerful and broadly used means of non-invasive... more Functional magnetic resonance imaging (fMRI) is a powerful and broadly used means of non-invasively mapping human brain activity. However fMRI is an indirect measure that rests upon a mapping from neuronal activity to the blood oxygen level dependent (BOLD) signal via hemodynamic effects. The quality of estimated neuronal activity hinges on the validity of the hemodynamic model employed. Recent work has demonstrated that the hemodynamic response has non-separable spatiotemporal dynamics, a key property that is not implemented in existing fMRI analysis frameworks. Here both simulated and empirical data are used to demonstrate that using a physiologically based model of the spatiotemporal hemodynamic response function (stHRF) results in a quantitative improvement of the estimated neuronal response relative to unphysical space-time separable forms. To achieve this, an integrated spatial and temporal deconvolution is established using a recently developed stHRF. Simulated data allows the variation of key parameters such as noise and the spatial complexity of the neuronal drive, while knowing the neuronal input. The results demonstrate that the use of a spatiotemporally integrated HRF can avoid "ghost" neuronal responses that can otherwise be falsely inferred. Applying the spatiotemporal deconvolution to high resolution fMRI data allows the recovery of neuronal responses that are consistent with independent electrophysiological measures.
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NeuroImage, 2013
The hippocampus is a neuroanatomical structure that has been widely studied in the context of lea... more The hippocampus is a neuroanatomical structure that has been widely studied in the context of learning, memory, stress, and neurodegeneration. Neuroanatomically, the hippocampus is subdivided into several subfields with intricate morphologies and complex three-dimensional relationships. Recent studies have demonstrated that the identification of different subfields is possible with high-resolution and -contrast image volumes acquired using ex vivo specimens in a small bore 9.4 T scanner and, more recently, in vivo, at 7 T. In these studies, the neuroanatomical definitions of boundaries between subfields are based upon salient differences in image contrast. Typically, the definition of subfields has not been possible using commonly available magnetic resonance (MR) scanners (i.e.: 1.5 or 3T) due to resolution and contrast limitations. To overcome the limited availability of post-mortem specimens and expertise in state-of-the-art high-field imaging, we propose a coupling of MR acquisition and detailed segmentation techniques that allow for the reliable identification of hippocampal anatomy (including subfields). High-resolution and -contrast T1- and T2-weighted image volumes were acquired from 5 volunteers (2 male; 3 female; age range: 29-57, avg. 37) using a clinical research-grade 3T scanner and have final super-sampled isotropic voxel dimensions of 0.3mm. We demonstrate that by using these acquisition techniques, our data results in contrast-to-noise ratios that compare well with high-resolution images acquired with long scan times using post-mortem data at higher field strengths. For the subfields, the cornus ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, stratum radiatum/stratum lacunosum/stratum moleculare, and subiculum were all labeled as separate structures. Hippocampal volumes are reported for each of the substructures and the hippocampus as a whole (range for hippocampus: 2456.72-3325.02 mm(3)). Intra-rater reliability of our manual segmentation protocol demonstrates high reliability for the whole hippocampus (mean Dice Kappa of 0.91; range 0.90-0.92) and for each of the subfields (range of Dice Kappas: 0.64-0.83). We demonstrate that our reliability is better than the Dice Kappas produced by simulating the following errors: a translation by a single voxel in all cardinal directions and 1% volumetric shrinkage and expansion. The completed hippocampal atlases are available freely online (info2.camh.net/kf-tigr/index.php/Hippocampus) and can be coupled with novel computational neuroanatomy techniques that will allow for them to be customized to the unique neuroanatomy of different subjects, and ultimately be utilized in different analysis pipelines.
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Journal of Vision, 2012
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Journal of Cognitive Neuroscience, 2014
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