Comprehensive integration of structural and functional connectivity data is required to model bra... more Comprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing data (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations, (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by co...
Abstract The biocompatibility of macromolecular therapeutics for enhanced passive permeation and ... more Abstract The biocompatibility of macromolecular therapeutics for enhanced passive permeation and retention remains a concern due to release kinetics or surface area properties. Dendritic conjugates functionalized with paramagnetic metal chelate with diameters less than (
<strong>Macaque atlas: the SARM</strong> <strong>Overview</strong> Here w... more <strong>Macaque atlas: the SARM</strong> <strong>Overview</strong> Here we present the Subcortical Atlas of the Rhesus Macaque (SARM). This atlas is defined in the coordinates/space of the NMT v2 template, described here: Macaque template: NMT v2 (current). <strong>Contents</strong> Digitized anatomical atlases are crucial for examining brain structure and the functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we created a complete parcellation of the rhesus macaque subcortex using high-resolution <em>ex vivo structural </em>imaging and histological data. The structural scan was warped to the NIMH Macaque Template (NMT v2), an <em>in vivo</em> population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM). The NMT v2 has several forms and variants (based on symmetry/asymmetry, field-of-view, and voxel size), and for each of these there is an accompanying SARM. Using an updated version of the Rhesus Monkey Brain in Stereotaxic Coordinates (Paxinos et al., 2009; Paxinos et al., in preparation) for guidance, the SARM features 6 parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies. The SARM is distributed as a single dataset with six sub-volumes, whereby SARM Level 1 is volume "[0]" and Level 6 is volume "[5]". The distribution also includes a binary SARM mask file. The download includes a CSV table file of the hierarchically-organized ROI labels. This can be viewed as a simple text file or within any spreadsheet software, such as Microsoft Excel. <strong>Download</strong> The SARM can be downloaded directly here, and it is also distributed as part of the NMT v2 download. For each form/variant of the NMT, there is a matching SARM dataset, as well. To download and unpack the datasets, please see the instructions… … here for the <strong>symmetric</strong> from: Download symmetric NMT v2 datasets … here for the <strong>asymmetric</strong> [...]
Direct imaging of macrovascular and microvascular contributions to BOLD fMRI in layers IV-V of th... more Direct imaging of macrovascular and microvascular contributions to BOLD fMRI in layers IV-V of the rat whisker-barrel cortex
Digitized neuroanatomical atlases are crucial for localizing brain structures and analyzing funct... more Digitized neuroanatomical atlases are crucial for localizing brain structures and analyzing functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we have created a comprehensive parcellation of the rhesus macaque subcortex using a high-resolution ex vivo structural imaging scan. The structural scan and its parcellation were warped to the updated NIMH Macaque Template (NMT v2), an in vivo population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM). The subcortical parcellation and nomenclature reflect those of the 4th edition of the Rhesus Monkey Brain in Stereotaxic Coordinates (RMBSC4; Paxinos et al., in preparation). The SARM features six parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies. As a test, we ran a functional localizer for the dorsal lateral geniculate (DLG) nucleus in three macaques and...
An amendment to this paper has been published and can be accessed via a link at the top of the pa... more An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Subcortical nuclei and other deep brain structures are known to play an important role in the reg... more Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep br...
The comprehensive integration of structural and functional connectivity data is required for the ... more The comprehensive integration of structural and functional connectivity data is required for the accurate modeling of brain functions. While resources for studying structural connectivity of non-human primate marmoset brains already exist, their integration with functional connectivity data has remained unavailable. Therefore, we present a comprehensive resource for marmoset brain mapping, which integrates the largest awake resting-state fMRI dataset to date (39 marmosets, 709 runs, and 12053 mins), cellular- level neuronal-tracing dataset (52 marmosets and 143 injections), and multi-resolution diffusion MRI dataset. The combination of these data into the same MRI space allowed us to 1). map the fine-detailed functional networks and cortical parcellations; 2). develop a deep-learning-based parcellation generator to preserve the topographical organization of functional connectivity and reflect individual variabilities; 3). investigate the structural basis underlying functional connec...
Object: A real-time functional magnetic resonance imaging (fMRI) feedback during ventral intermed... more Object: A real-time functional magnetic resonance imaging (fMRI) feedback during ventral intermediate nucleus (VIM) deep brain stimulation (DBS) under general anesthesia (or “asleep” DBS) does not exist. We hypothesized that it was feasible to acquire a reliable and responsive fMRI during asleep VIM DBS surgery.Methods: We prospectively enrolled 10 consecutive patients who underwent asleep DBS for the treatment of medication-refractory essential tremor. Under general anesthesia, we acquired resting-state functional MRI immediately before and after the cannula insertion. Reliability was determined by a temporal signal-to-noise-ratio >100. Responsiveness was determined based on the fMRI signal change upon insertion of the cannula to the VIM.Results: It was feasible to acquire reliable fMRI during asleep DBS surgery. The fMRI signal was responsive to the brain cannula insertion, revealing a reduction in the tremor network's functional connectivity, which did not reach statistica...
Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience... more Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.
Comprehensive integration of structural and functional connectivity data is required to model bra... more Comprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing data (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations, (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by co...
Abstract The biocompatibility of macromolecular therapeutics for enhanced passive permeation and ... more Abstract The biocompatibility of macromolecular therapeutics for enhanced passive permeation and retention remains a concern due to release kinetics or surface area properties. Dendritic conjugates functionalized with paramagnetic metal chelate with diameters less than (
<strong>Macaque atlas: the SARM</strong> <strong>Overview</strong> Here w... more <strong>Macaque atlas: the SARM</strong> <strong>Overview</strong> Here we present the Subcortical Atlas of the Rhesus Macaque (SARM). This atlas is defined in the coordinates/space of the NMT v2 template, described here: Macaque template: NMT v2 (current). <strong>Contents</strong> Digitized anatomical atlases are crucial for examining brain structure and the functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we created a complete parcellation of the rhesus macaque subcortex using high-resolution <em>ex vivo structural </em>imaging and histological data. The structural scan was warped to the NIMH Macaque Template (NMT v2), an <em>in vivo</em> population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM). The NMT v2 has several forms and variants (based on symmetry/asymmetry, field-of-view, and voxel size), and for each of these there is an accompanying SARM. Using an updated version of the Rhesus Monkey Brain in Stereotaxic Coordinates (Paxinos et al., 2009; Paxinos et al., in preparation) for guidance, the SARM features 6 parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies. The SARM is distributed as a single dataset with six sub-volumes, whereby SARM Level 1 is volume "[0]" and Level 6 is volume "[5]". The distribution also includes a binary SARM mask file. The download includes a CSV table file of the hierarchically-organized ROI labels. This can be viewed as a simple text file or within any spreadsheet software, such as Microsoft Excel. <strong>Download</strong> The SARM can be downloaded directly here, and it is also distributed as part of the NMT v2 download. For each form/variant of the NMT, there is a matching SARM dataset, as well. To download and unpack the datasets, please see the instructions… … here for the <strong>symmetric</strong> from: Download symmetric NMT v2 datasets … here for the <strong>asymmetric</strong> [...]
Direct imaging of macrovascular and microvascular contributions to BOLD fMRI in layers IV-V of th... more Direct imaging of macrovascular and microvascular contributions to BOLD fMRI in layers IV-V of the rat whisker-barrel cortex
Digitized neuroanatomical atlases are crucial for localizing brain structures and analyzing funct... more Digitized neuroanatomical atlases are crucial for localizing brain structures and analyzing functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we have created a comprehensive parcellation of the rhesus macaque subcortex using a high-resolution ex vivo structural imaging scan. The structural scan and its parcellation were warped to the updated NIMH Macaque Template (NMT v2), an in vivo population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM). The subcortical parcellation and nomenclature reflect those of the 4th edition of the Rhesus Monkey Brain in Stereotaxic Coordinates (RMBSC4; Paxinos et al., in preparation). The SARM features six parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies. As a test, we ran a functional localizer for the dorsal lateral geniculate (DLG) nucleus in three macaques and...
An amendment to this paper has been published and can be accessed via a link at the top of the pa... more An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Subcortical nuclei and other deep brain structures are known to play an important role in the reg... more Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep br...
The comprehensive integration of structural and functional connectivity data is required for the ... more The comprehensive integration of structural and functional connectivity data is required for the accurate modeling of brain functions. While resources for studying structural connectivity of non-human primate marmoset brains already exist, their integration with functional connectivity data has remained unavailable. Therefore, we present a comprehensive resource for marmoset brain mapping, which integrates the largest awake resting-state fMRI dataset to date (39 marmosets, 709 runs, and 12053 mins), cellular- level neuronal-tracing dataset (52 marmosets and 143 injections), and multi-resolution diffusion MRI dataset. The combination of these data into the same MRI space allowed us to 1). map the fine-detailed functional networks and cortical parcellations; 2). develop a deep-learning-based parcellation generator to preserve the topographical organization of functional connectivity and reflect individual variabilities; 3). investigate the structural basis underlying functional connec...
Object: A real-time functional magnetic resonance imaging (fMRI) feedback during ventral intermed... more Object: A real-time functional magnetic resonance imaging (fMRI) feedback during ventral intermediate nucleus (VIM) deep brain stimulation (DBS) under general anesthesia (or “asleep” DBS) does not exist. We hypothesized that it was feasible to acquire a reliable and responsive fMRI during asleep VIM DBS surgery.Methods: We prospectively enrolled 10 consecutive patients who underwent asleep DBS for the treatment of medication-refractory essential tremor. Under general anesthesia, we acquired resting-state functional MRI immediately before and after the cannula insertion. Reliability was determined by a temporal signal-to-noise-ratio >100. Responsiveness was determined based on the fMRI signal change upon insertion of the cannula to the VIM.Results: It was feasible to acquire reliable fMRI during asleep DBS surgery. The fMRI signal was responsive to the brain cannula insertion, revealing a reduction in the tremor network's functional connectivity, which did not reach statistica...
Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience... more Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.
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