An MRI based average macaque monkey stereotaxic atlas and space (MNI monkey space)

Multiscale chemogenetic dissection of fronto-temporal top-down regulation for object memory in primates

Visual object memory is a fundamental element of various cognitive abilities, and the underlying neural mechanisms have been extensively examined especially in the anterior temporal cortex of primates. However, both macroscopic large-scale functional network in which this region is embedded and microscopic neuron-level dynamics of top-down regulation it receives for object memory remains elusive. Here, we identified the orbitofrontal node as a critical partner of the anterior temporal node for object memory by combining whole-brain functional imaging during rest and a short-term object memory task in male macaques. Focal chemogenetic silencing of the identified orbitofrontal node downregulated both the local orbitofrontal and remote anterior temporal nodes during the task, in association with deteriorated mnemonic, but not perceptual, performance. Furthermore, imaging-guided neuronal recordings in the same monkeys during the same task causally revealed that orbitofrontal top-down modulation enhanced stimulus-selective mnemonic signal in individual anterior temporal neurons while leaving bottom-up perceptual signal unchanged. Furthermore, similar activity difference was also observed between correct and mnemonic error trials before silencing, suggesting its behavioral relevance. These multifaceted but convergent results provide a multiscale causal understanding of dynamic top-down regulation of the anterior temporal cortex along the ventral fronto-temporal network underpinning short-term object memory in primates.

An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys

BACKGROUND

High-precision neurosurgical targeting in nonhuman primates (NHPs) often requires presurgical anatomical mapping with noninvasive neuroimaging techniques (MRI, CT, PET), allowing for translation of individual anatomical coordinates to surgical stereotaxic apparatus. Given the varied tissue contrasts that these imaging techniques produce, precise alignment of imaging-based coordinates to surgical apparatus can be cumbersome. MRI-compatible stereotaxis with radiopaque fiducial markers offer a straight-forward and reliable solution, but existing commercial options do not fit in conformal head coils that maximize imaging quality.

NEW METHOD

We developed a compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta, Macaca fascicularis, and Cebus apella) that allows multimodal alignment through technique-specific fiducial markers.

COMPARISON WITH EXISTING METHODS

With the express purpose of compatibility with clinically available MRI, CT, and PET systems, the frame is no larger than a human head, while allowing for imaging NHPs in the supinated position. This design requires no marker implantation, special software, or additional knowledge other than the operation of a common large animal stereotaxis.

RESULTS

We demonstrated the applicability of this 3D-printable apparatus across a diverse set of experiments requiring presurgical planning: 1) We demonstrate the accuracy of the fiducial system through a within-MRI cannula insertion and subcortical injection of a viral vector. 2) We also demonstrated accuracy of multimodal (MRI and CT) alignment and coordinate transfer to guide a surgical robot electrode implantation for deep-brain electrophysiology.

CONCLUSIONS

The computer-aided design files and engineering drawings are publicly available, with the modular design allowing for low cost and manageable manufacturing.

Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention

Neurons from multiple prefrontal areas encode several key variables of social gaze interaction. To explore the causal roles of the primate prefrontal cortex in real-life gaze interaction, we applied weak closed-loop microstimulations that were precisely triggered by specific social gaze events. Microstimulations of the orbitofrontal cortex, but not the dorsomedial prefrontal cortex or the anterior cingulate cortex, enhanced momentary dynamic social attention in the spatial dimension by decreasing the distance of fixations relative to a partner's eyes and in the temporal dimension by reducing the inter-looking interval and the latency to reciprocate the other's directed gaze. By contrast, on a longer timescale, microstimulations of the dorsomedial prefrontal cortex modulated inter-individual gaze dynamics relative to one's own gaze positions. These findings demonstrate that multiple regions in the primate prefrontal cortex may serve as functionally accessible nodes in controlling different aspects of dynamic social attention and suggest their potential for a therapeutic brain interface.

From imaging to precision: low cost and accurate determination of stereotactic coordinates for brain surgery Sapajus apella using MRI

The capuchin monkey (Sapajus apella), a New World monkey species, exhibits prominent characteristics that make it an ideal model for neuroscience research. These characteristics include its phylogenetic traits, telencephalization coefficient, anatomical structures and pathways, genetic profile, immune responses, cognitive abilities, and complex behavioral repertoires. Traditionally, methodologies for stereotactic neurosurgery in research models have relied on the use of brain atlases. However, this approach can lead to errors due to the considerable variation in brain size and shape among individual monkeys. To address this issue, we developed a protocol for deriving individual coordinates for each monkey using a straightforward and relatively inexpensive method involving MRI imaging. Our protocol utilizes a specially designed, 3D-printed stereotactic head-holder that is safe to use with an MR magnet, non-invasive placement of fiducial markers, and post-processing with open-source software. This approach enhances MRI data visualization, improves anatomical targeting, and refines the design of neurosurgical experiments. Our technique could also prove beneficial in other areas of neuroscience research that require accurate calculation of stereotaxic coordinates. Furthermore, it could be useful for other nonhuman primate species for which brain atlases are typically unavailable.

Human Embryonic Stem Cell-Derived Immature Midbrain Dopaminergic Neurons Transplanted in Parkinsonian Monkeys

Human embryonic stem cells (hESCs) differentiate into specialized cells, including midbrain dopaminergic neurons (DANs), and Non-human primates (NHPs) injected with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine develop some alterations observed in Parkinson's disease (PD) patients. Here, we obtained well-characterized DANs from hESCs and transplanted them into two parkinsonian monkeys to assess their behavioral and imaging changes. DANs from hESCs expressed dopaminergic markers, generated action potentials, and released dopamine (DA) in vitro. These neurons were transplanted bilaterally into the putamen of parkinsonian NHPs, and using magnetic resonance imaging techniques, we calculated the fractional anisotropy (FA) and mean diffusivity (MD), both employed for the first time for these purposes, to detect in vivo axonal and cellular density changes in the brain. Likewise, positron-emission tomography scans were performed to evaluate grafted DANs. Histological analyses identified grafted DANs, which were quantified stereologically. After grafting, animals showed signs of partially improved motor behavior in some of the HALLWAY motor tasks. Improvement in motor evaluations was inversely correlated with increases in bilateral FA. MD did not correlate with behavior but presented a negative correlation with FA. We also found higher 11C-DTBZ binding in positron-emission tomography scans associated with grafts. Higher DA levels measured by microdialysis after stimulation with a high-potassium solution or amphetamine were present in grafted animals after ten months, which has not been previously reported. Postmortem analysis of NHP brains showed that transplanted DANs survived in the putamen long-term, without developing tumors, in immunosuppressed animals. Although these results need to be confirmed with larger groups of NHPs, our molecular, behavioral, biochemical, and imaging findings support the integration and survival of human DANs in this pre-clinical PD model.

Distinct Lateral Prefrontal Regions Are Organized in an Anterior-Posterior Functional Gradient

The dorsolateral prefrontal cortex (dlPFC) is composed of multiple anatomically defined regions involved in higher-order cognitive processes, including working memory and selective attention. It is organized in an anterior-posterior global gradient where posterior regions track changes in the environment, whereas anterior regions support abstract neural representations. However, it remains unknown if such a global gradient results from a smooth gradient that spans regions or an emergent property arising from functionally distinct regions, that is, an areal gradient. Here, we recorded single neurons in the dlPFC of nonhuman primates trained to perform a memory-guided saccade task with an interfering distractor and analyzed their physiological properties along the anterior-posterior axis. We found that these physiological properties were best described by an areal gradient. Further, population analyses revealed that there is a distributed representation of spatial information across the dlPFC. Our results validate the functional boundaries between anatomically defined dlPFC regions and highlight the distributed nature of computations underlying working memory across the dlPFC.SIGNIFICANCE STATEMENT Activity of frontal lobe regions is known to possess an anterior-posterior functional gradient. However, it is not known whether this gradient is the result of individual brain regions organized in a gradient (like a staircase), or a smooth gradient that spans regions (like a slide). Analysis of physiological properties of individual neurons in the primate frontal regions suggest that individual regions are organized as a gradient, rather than a smooth gradient. At the population level, working memory was more prominent in posterior regions, although it was also present in anterior regions. This is consistent with the functional segregation of brain regions that is also observed in other systems (i.e., the visual system).

Non-human primate models of focal cortical ischemia for neuronal replacement therapy

Despite the high prevalence, stroke remains incurable due to the limited regeneration capacity in the central nervous system. Neuronal replacement strategies are highly diverse biomedical fields that attempt to replace lost neurons by utilizing exogenous stem cell transplants, biomaterials, and direct neuronal reprogramming. Although these approaches have achieved encouraging outcomes mostly in the rodent stroke model, further preclinical validation in non-human primates (NHP) is still needed prior to clinical trials. In this paper, we briefly review the recent progress of promising neuronal replacement therapy in NHP stroke studies. Moreover, we summarize the key characteristics of the NHP as highly valuable translational tools and discuss (1) NHP species and their advantages in terms of genetics, physiology, neuroanatomy, immunology, and behavior; (2) various methods for establishing NHP focal ischemic models to study the regenerative and plastic changes associated with motor functional recovery; and (3) a comprehensive analysis of experimentally and clinically accessible outcomes and a potential adaptive mechanism. Our review specifically aims to facilitate the selection of the appropriate NHP cortical ischemic models and efficient prognostic evaluation methods in preclinical stroke research design of neuronal replacement strategies.

Cytoarchitectonic, receptor distribution and functional connectivity analyses of the macaque frontal lobe

Based on quantitative cyto- and receptor architectonic analyses, we identified 35 prefrontal areas, including novel subdivisions of Walker's areas 10, 9, 8B, and 46. Statistical analysis of receptor densities revealed regional differences in lateral and ventrolateral prefrontal cortex. Indeed, structural and functional organization of subdivisions encompassing areas 46 and 12 demonstrated significant differences in the interareal levels of α2 receptors. Furthermore, multivariate analysis included receptor fingerprints of previously identified 16 motor areas in the same macaque brains and revealed 5 clusters encompassing frontal lobe areas. We used the MRI datasets from the non-human primate data sharing consortium PRIME-DE to perform functional connectivity analyses using the resulting frontal maps as seed regions. In general, rostrally located frontal areas were characterized by bigger fingerprints, that is, higher receptor densities, and stronger regional interconnections. Whereas more caudal areas had smaller fingerprints, but showed a widespread connectivity pattern with distant cortical regions. Taken together, this study provides a comprehensive insight into the molecular structure underlying the functional organization of the cortex and, thus, reconcile the discrepancies between the structural and functional hierarchical organization of the primate frontal lobe. Finally, our data are publicly available via the EBRAINS and BALSA repositories for the entire scientific community.

versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database

The lack of "gold standards" in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, as their cytoarchitecture is closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a modular pipeline implemented in Nextflow, designed for robustness and scalability. The pipeline is tailored to in vivo NHP DWI at any spatial resolution; it allows for maintainability and customization. Processes and workflows are implemented using cutting-edge and state-of-the-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD), and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI), and DWI of NHP brains. This dataset includes images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site's data, to ensure that our implementation has minimal impact on the variability observed in subsequent analyses. We report very high reproducibility for the majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME-DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms capable of managing the variability induced in imaging due to differences in scanner models and/or vendors.

The relevance of the unique anatomy of the human prefrontal operculum to the emergence of speech

Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy compared to chimpanzees and other primates that may provide an explanation of changes that occurred to enable the capacity for speech. That feature is the Prefrontal extent of the Frontal Operculum (PFOp) region, which is located in the ventrolateral prefrontal cortex, adjacent and ventromedial to the classical Broca's area. We also show that, in chimpanzees, individuals with the most human-like PFOp, particularly in the left hemisphere, have greater oro-facial and vocal motor control abilities. This critical discovery, when combined with recent paleontological evidence, suggests that the PFOp is a recently evolved feature of human cortical structure (perhaps limited to the genus Homo) that emerged in response to increasing selection for cognitive and motor functions evident in modern speech abilities.

A revised perspective on the evolution of the lateral frontal cortex in primates

Detailed neuroscientific data from macaque monkeys have been essential in advancing understanding of human frontal cortex function, particularly for regions of frontal cortex without homologs in other model species. However, precise transfer of this knowledge for direct use in human applications requires an understanding of monkey to hominid homologies, particularly whether and how sulci and cytoarchitectonic regions in the frontal cortex of macaques relate to those in hominids. We combine sulcal pattern analysis with resting-state functional magnetic resonance imaging and cytoarchitectonic analysis to show that old-world monkey brains have the same principles of organization as hominid brains, with the notable exception of sulci in the frontopolar cortex. This essential comparative framework provides insights into primate brain evolution and a key tool to drive translation from invasive research in monkeys to human applications.

Automatic brain extraction and brain tissues segmentation on multi-contrast animal MRI

For many neuroscience applications, brain extraction in MRI images is the first pre-processing step of a quantification pipeline. Once the brain is extracted, further post-processing calculations become faster, more specific and easier to implement and interpret. It is the case, for example, of functional MRI brain studies, or relaxation time mappings and brain tissues classifications to characterise brain pathologies. Existing brain extraction tools are mostly adapted to work on the human anatomy, this gives poor results when applied to animal brain images. We have developed an atlas-based Veterinary Images Brain Extraction (VIBE) algorithm that encompasses a pre-processing step to adapt the atlas to the patient's image, and a subsequent registration step. We show that the brain extraction is achieved with excellent results in terms of Dice and Jaccard metrics. The algorithm is automatic, with no need to adapt the parameters in a broad range of situations: we successfully tested multiple MRI contrasts (T1-weighted, T2-weighted, T2-weighted FLAIR), all the acquisition planes (sagittal, dorsal, transverse), different animal species (dogs and cats) and canine cranial conformations (brachycephalic, mesocephalic, dolichocephalic). VIBE can be successfully extended to other animal species, provided that an atlas for that specific species exists. We show also how brain extraction, as a preliminary step, can help to segment brain tissues with a K-Means clustering algorithm.

A multimodal imaging-guided software for access to primate brains

Background

Imaging-guided access to the brain has become a routine procedure for various research and clinical applications, including drug administration, neurophysiological recording, and sampling tissue. Therefore, open-source software is required to handle such datasets in these specific applications.

New methods

Here, we proposed an open-source tool utilizing different imaging modalities for automating the steps to access the brain. This tool provides means for easily calculating the coordination of the area of interest concerning a specific point of entry. The source and documentation are available at this link.

Results

We have used this software for three different applications: electrophysiological recording, drug infusion in the nonhuman primate brain, and guided biopsy procedure in the human brain. We performed a neural recording of two monkeys' prefrontal cortex and inferior temporal cortex using this software in submillimeter resolution. We also applied our procedure for infusion in the putamen and caudate nuclei in both hemispheres of another group of rhesus monkeys with histological proof in one animal. More so, we validated this software in the human subjects that underwent biopsy surgery with the commercial software used in human biopsy surgery.

Comparison with existing methods

Our software uses different imaging modalities by co-registering them. This will provide structural details of the skull and brain tissue. We can calculate each brain region's coordination at the point of entry by re-slicing the images. Atlas-based image segmentation were implemented in our software. Three mentioned applications of our software in neuroscience will be further discussed in this paper.

Conclusion

In our procedure, working with different imaging modalities provides a precise estimation of the specific region in the brain related to the location of implants or stereotaxic frames. There is no limitation to using metal implants in this procedure.

Automatic macaque brain segmentation based on 7T MRI

BACKGROUND

In monkey neuroimaging, particularly magnetic resonance imaging (MRI) studies, quick and accurate automatic macaque brain segmentation is essential. However, there are few processing and analysis tools dedicated to automatic brain tissue segmentation and labeling of the macaque brain on a subject-specific basis. As a result, currently most adopted methods are through direct implementation of existing tools that have been designed for human brain. However, the operation steps combining different functional modules of a variety of processing and analysis tool software are inevitably complicated, cumbersome, time-consuming and labor-intensive.

NEW METHOD

In this study, we proposed a novel quick and accurate automatic macaque brain segmentation method based on multi-atlas registration and majority-vote algorithm. First, the single-atlas method based on S-HAMMER is used to register each template image of the reference atlas set (including brain tissue labeled images and brain anatomical structure labeled images) to the preprocessed image to be segmented. Thus, we obtain the corresponding deformation field and spatially transform the labeled image, and then get multiple segmentation results by local weighted voting method, which perform label fusion to obtain the final labeled images of brain structures segmentation result.

RESULTS

By collecting high SNR and high spatial resolution images of macaque brain images from our 7T human MRI scanner, we have constructed two brain templates for each individual macaque subject, and macaque brain tissues and brain anatomical structure by one-atlas method. However, segmentation result of single-atlas method is not much accurate in some brain tissue area. It takes about 2 h and need more manual correction for segmentation. Automatic segmentation of macaque brain structure based on multi-atlas method was reasonably successful, the accuracy of segmentation was greatly improved without manual correction. Also, the proposed method provided good tissue fitting to V1 with smooth and continuous boundary. The Dice similarity of multi-atlas method showing 3.24%, 4.24%, 2.55%, 2.85%, 3.05%, and 0.35% improvement in image slices of 63, 66, 70, 71, 99 and 100, respectively. The entire processing time for the construction of a single template map took ~40 min.

CONCLUSIONS

This study proposed a novel automatic segmentation method of individual macaque brain structure based on multi-atlas registration method, which is concise and reliable. It may offer a valuable tool to applications in the field of brain and neuroscience research using the macaque as an experimental animal model.

Population-Average Brain Templates and Application to Automated Voxel-Wise Analysis Pipelines for Cynomolgus Macaque

The growing number of neuroimaging studies of cynomolgus macaques require extending existing templates to facilitate species-specific application of voxel-wise neuroimaging methodologies. This study aimed to create population-averaged structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) templates for the cynomolgus macaques and apply the templates in fully automated voxel-wise analyses. We presented the development of symmetric and asymmetric MRI and DTI templates from a sample of 63 young male cynomolgus monkeys with the use of optimized template creation approaches. We also generated the associated average tissue probability maps and Diffeomorphic Anatomical Registration using Exponentiated Lie Algebra templates for use with the Statistical Parametric Mapping (SPM), as well as the average fractional anisotropy/skeleton targets for incorporation into tract-based spatial statistics (TBSS) framework. Both asymmetric and symmetric templates in a standardized coordinate space demonstrated low bias and high contrast. Fully automated processing using SPM was accomplished for all native MRI datasets and demonstrated outstanding performance regarding skull-stripping, segmentation, and normalization when using the MRI templates. Automated normalization to the DTI template was excellently achieved for all native DTI images using the TBSS pipeline. The cynomolgus MRI and DTI templates are anticipated to provide a common platform for precise single-subject data analysis and facilitate comparison of neuroimaging findings in cynomolgus monkeys across studies and sites. It is also hoped that the procedures of template creation and fully-automated voxel-wise frameworks will provide a straightforward avenue for investigating brain function, development, and neuro-psychopathological disorders in non-human primate models.

Intra-Areal Visual Topography in Primate Brains Mapped with Probabilistic Tractography of Diffusion-Weighted Imaging

Noninvasive diffusion-weighted magnetic resonance imaging (dMRI) can be used to map the neural connectivity between distinct areas in the intact brain, but the standard resolution achieved fundamentally limits the sensitivity of such maps. We investigated the sensitivity and specificity of high-resolution postmortem dMRI and probabilistic tractography in rhesus macaque brains to produce retinotopic maps of the lateral geniculate nucleus (LGN) and extrastriate cortical visual area V5/MT based on their topographic connections with the previously established functional retinotopic map of primary visual cortex (V1). We also replicated the differential connectivity of magnocellular and parvocellular LGN compartments with V1 across visual field positions. Predicted topographic maps based on dMRI data largely matched the established retinotopy of both LGN and V5/MT. Furthermore, tractography based on in vivo dMRI data from the same macaque brains acquired at standard field strength (3T) yielded comparable topographic maps in many cases. We conclude that tractography based on dMRI is sensitive enough to reveal the intrinsic organization of ordered connections between topographically organized neural structures and their resultant functional organization.

Anatomical and functional connectivity support the existence of a salience network node within the caudal ventrolateral prefrontal cortex

Three large-scale networks are considered essential to cognitive flexibility: the ventral and dorsal attention (VANet and DANet) and salience (SNet) networks. The ventrolateral prefrontal cortex (vlPFC) is a known component of the VANet and DANet, but there is a gap in the current knowledge regarding its involvement in the SNet. Herein, we used a translational and multimodal approach to demonstrate the existence of a SNet node within the vlPFC. First, we used tract-tracing methods in non-human primates (NHP) to quantify the anatomical connectivity strength between different vlPFC areas and the frontal and insular cortices. The strongest connections were with the dorsal anterior cingulate cortex (dACC) and anterior insula (AI) - the main cortical SNet nodes. These inputs converged in the caudal area 47/12, an area that has strong projections to subcortical structures associated with the SNet. Second, we used resting-state functional MRI (rsfMRI) in NHP data to validate this SNet node. Third, we used rsfMRI in the human to identify a homologous caudal 47/12 region that also showed strong connections with the SNet cortical nodes. Taken together, these data confirm a SNet node in the vlPFC, demonstrating that the vlPFC contains nodes for all three cognitive networks: VANet, DANet, and SNet. Thus, the vlPFC is in a position to switch between these three networks, pointing to its key role as an attentional hub. Its additional connections to the orbitofrontal, dorsolateral, and premotor cortices, place the vlPFC at the center for switching behaviors based on environmental stimuli, computing value, and cognitive control.

Deep brain stimulation of the thalamus restores signatures of consciousness in a nonhuman primate model

Loss of consciousness is associated with the disruption of long-range thalamocortical and corticocortical brain communication. We tested the hypothesis that deep brain stimulation (DBS) of central thalamus might restore both arousal and awareness following consciousness loss. We applied anesthesia to suppress consciousness in nonhuman primates. During anesthesia, central thalamic stimulation induced arousal in an on-off manner and increased functional magnetic resonance imaging activity in prefrontal, parietal, and cingulate cortices. Moreover, DBS restored a broad dynamic repertoire of spontaneous resting-state activity, previously described as a signature of consciousness. None of these effects were obtained during the stimulation of a control site in the ventrolateral thalamus. Last, DBS restored a broad hierarchical response to auditory violations that was disrupted under anesthesia. Thus, DBS restored the two dimensions of consciousness, arousal and conscious access, following consciousness loss, paving the way to its therapeutical translation in patients with disorders of consciousness.

Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain

Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses.

Longitudinal changes of deep gray matter shape in multiple sclerosis

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Specific shape changes over time occur at the bilateral ventrolateral pallidal and the left posterolateral striatal surface in relapse-onset multiple sclerosis.

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These shape changes over time were not associated with disease progression.

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The average shape of deep gray matter structures was associated with the patients’ average disease severity as well as white matter lesion-load.

Objective

This study aimed to investigate longitudinal deep gray matter (DGM) shape changes and their relationship with measures of clinical disability and white matter lesion-load in a large multiple sclerosis (MS) cohort.

Materials and Methods

A total of 230 MS patients (179 relapsing-remitting, 51 secondary progressive; baseline age 44.5 ± 11.3 years; baseline disease duration 12.99 ± 9.18) underwent annual clinical and MRI examinations over a maximum of 6 years (mean 4.32 ± 2.07 years). The DGM structures were segmented on the T1-weighted images using the “Multiple Automatically Generated Templates” brain algorithm. White matter lesion-load was measured on T2-weighted MRI. Clinical examination included the expanded disability status scale, 9-hole peg test, timed 25-foot walk test, symbol digit modalities test and paced auditory serial addition test. Vertex‐wise longitudinal analysis of DGM shapes was performed using linear mixed effect models and evaluated the association between average/temporal changes of DGM shapes with average/temporal changes of clinical measurements, respectively.

Results

A significant shrinkage over time of the bilateral ventrolateral pallidal and the left posterolateral striatal surface was observed, whereas no significant shape changes over time were observed at the bilateral thalamic and right striatal surfaces. Higher average lesion-load was associated with an average inwards displacement of the global thalamic surface with relative sparing on the posterior side (slight left-side predominance), the antero-dorso-lateral striatal surfaces bilaterally (symmetric on both sides) and the antero-lateral pallidal surface (left-side predominance). There was also an association between shrinkage of large lateral DGM surfaces with higher clinical motor and cognitive disease severity. However, there was no correlation between any DGM shape changes over time and measurements of clinical progression or lesion-load changes over time.

Conclusions

This study showed specific shape change of DGM structures occurring over time in relapse-onset MS. Although these shape changes over time were not associated with disease progression, we demonstrated a link between DGM shape and the patients’ average disease severity as well as white matter lesion-load.

Continuous subcellular resolution three-dimensional imaging on intact macaque brain

To decipher the organizational logic of complex brain circuits, it is important to chart long-distance pathways while preserving micron-level accuracy of local network. However, mapping the neuronal projections with individual-axon resolution in the large and complex primate brain is still challenging. Herein, we describe a highly efficient pipeline for three-dimensional mapping of the entire macaque brain with subcellular resolution. The pipeline includes a novel poly-N-acryloyl glycinamide (PNAGA)-based embedding method for long-term structure and fluorescence preservation, high-resolution and rapid whole-brain optical imaging, and image post-processing. The cytoarchitectonic information of the entire macaque brain was acquired with a voxel size of 0.32 μm × 0.32 μm × 10 μm, showing its anatomical structure with cell distribution, density, and shape. Furthermore, thanks to viral labeling, individual long-distance projection axons from the frontal cortex were for the first time reconstructed across the entire brain hemisphere with a voxel size of 0.65 μm × 0.65 μm × 3 μm. Our results show that individual cortical axons originating from the prefrontal cortex simultaneously target multiple brain regions, including the visual cortex, striatum, thalamus, and midbrain. This pipeline provides an efficient method for cellular and circuitry investigation of the whole macaque brain with individual-axon resolution, and can shed light on brain function and disorders.

Longitudinal brain atlases of early developing cynomolgus macaques from birth to 48 months of age

Longitudinal brain imaging atlases with densely sampled time-points and ancillary anatomical information are of fundamental importance in studying early developmental characteristics of human and non-human primate brains during infancy, which feature extremely dynamic imaging appearance, brain shape and size. However, for non-human primates, which are highly valuable animal models for understanding human brains, the existing brain atlases are mainly developed based on adults or adolescents, denoting a notable lack of temporally densely-sampled atlases covering the dynamic early brain development. To fill this critical gap, in this paper, we construct a comprehensive set of longitudinal brain atlases and associated tissue probability maps (gray matter, white matter, and cerebrospinal fluid) with totally 12 time-points from birth to 4 years of age (i.e., 1, 2, 3, 4, 5, 6, 9, 12, 18, 24, 36, and 48 months of age) based on 175 longitudinal structural MRI scans from 39 typically-developing cynomolgus macaques, by leveraging state-of-the-art computational techniques tailored for early developing brains. Furthermore, to facilitate region-based analysis using our atlases, we also provide two popular hierarchy parcellations, i.e., cortical hierarchy maps (6 levels) and subcortical hierarchy maps (6 levels), on our longitudinal macaque brain atlases. These early developing atlases, which have the densest time-points during infancy (to the best of our knowledge), will greatly facilitate the studies of macaque brain development.

Species and individual differences and connectional asymmetry of Broca's area in humans and macaques

To reveal the connectional specialization of the Broca's area (or its homologue), voxel-wise inter-species and individual differences, and inter-hemispheric asymmetry were respectively inspected in humans and macaques at both whole-brain connectivity and single tract levels. It was discovered that the developed connectivity blueprint approach is able to localize connectionally comparable voxels between the two species in Broca's area, whereas the quantitative differences between blueprints of locationally or connectionally corresponding voxels enable us to generate inter-hemispheric, inter-subject, and inter-species connectional variabilities, respectively. More importantly, the inter-species and inter-subject variabilities exhibited positive correlation in both two primates, and relatively higher variabilities were detected in the anatomically defined pars triangularis. By contrast, negative relationship was identified between the inter-species variability and hemispheric asymmetry in human brain. In particular, relatively higher asymmetry was revealed in the anatomically defined pars opercularis. Therefore, our novel findings demonstrated that pars triangularis, as compared to pars opercularis, might be a more active area during primate evolution, in which the brain connectivity and possible functions of pars triangularis show relatively higher degree in species specialization, yet lower in hemispheric specialization. Meanwhile, brain connectivity and possible functions of pars opercularis manifested an opposite pattern. At the tract level, functional roles related to the ventral stream in speech comprehension were relatively conservative and bilaterally organized, while those related to the dorsal stream in speech production show relatively higher species and hemispheric specializations.

Histology-driven model of the macaque motor hyperdirect pathway

Emerging appreciation for the hyperdirect pathway (HDP) as an important cortical glutamatergic input to the subthalamic nucleus (STN) has motivated a wide range of recent investigations on its role in motor control, as well as the mechanisms of subthalamic deep brain stimulation (DBS). However, the pathway anatomy and terminal arbor morphometry by which the HDP links cortical and subthalamic activity are incompletely understood. One critical hindrance to advancing understanding is the lack of anatomically detailed population models which can help explain how HDP pathway anatomy and neuronal biophysics give rise to spatiotemporal patterns of stimulus-response activity observed in vivo. Therefore, the goal of this study was to establish a population model of motor HDP axons through application of generative algorithms constrained by recent histology and imaging data. The products of this effort include a de novo macaque brain atlas, detailed statistical analysis of histological reconstructions of macaque motor HDP axons, and the generation of 10,000 morphometrically constrained synthetic motor HDP axons. The synthetic HDP axons exhibited a 3.8% mean error with respect to parametric distributions of the fiber target volume, total length, number of bifurcations, bifurcation angles, meander angles, and segment lengths measured in BDA-labeled HDP axon reconstructions. As such, this large population of synthetic motor HDP axons represents an anatomically based foundation for biophysical simulations that can be coupled to electrophysiological and/or behavioral measurements, with the goal of better understanding the role of the HDP in motor system activity.

MRI-based Parcellation and Morphometry of the Individual Rhesus Monkey Brain: the macaque Harvard-Oxford Atlas (mHOA), a translational system referencing a standardized ontology

Investigations of the rhesus monkey (Macaca mulatta) brain have shed light on the function and organization of the primate brain at a scale and resolution not yet possible in humans. A cornerstone of the linkage between non-human primate and human studies of the brain is magnetic resonance imaging, which allows for an association to be made between the detailed structural and physiological analysis of the non-human primate and that of the human brain. To further this end, we present a novel parcellation method and system for the rhesus monkey brain, referred to as the macaque Harvard-Oxford Atlas (mHOA), which is based on the human Harvard-Oxford Atlas (HOA) and grounded in an ontological and taxonomic framework. Consistent anatomical features were used to delimit and parcellate brain regions in the macaque, which were then categorized according to functional systems. This system of parcellation will be expanded with advances in technology and, like the HOA, will provide a framework upon which the results from other experimental studies (e.g., functional magnetic resonance imaging (fMRI), physiology, connectivity, graph theory) can be interpreted.

A fully segmented 3D anatomical atlas of a lizard brain

As the relevance of lizards in evolutionary neuroscience increases, so does the need for more accurate anatomical references. Moreover, the use of magnetic resonance imaging (MRI) in evolutionary neuroscience is becoming more widespread; this represents a fundamental methodological shift that opens new avenues of investigative possibility but also poses new challenges. Here, we aim to facilitate this shift by providing a three-dimensional segmentation atlas of the tawny dragon brain. The tawny dragon (Ctenophorus decresii) is an Australian lizard of increasing importance as a model system in ecology and, as a member of the agamid lizards, in evolution. Based on a consensus average 3D image generated from the MRIs of 13 male tawny dragon heads, we identify and segment 224 structures visible across the entire lizard brain. We describe the relevance of this atlas to the field of evolutionary neuroscience and propose further experiments for which this atlas can provide the foundation. This advance in defining lizard neuroanatomy will facilitate numerous studies in evolutionary neuroscience. The atlas is available for download as a supplementary material to this manuscript and through the Open Science Framework (OSF; https://doi.org/10.17605/OSF.IO/UJENQ ).

Using non-invasive neuroimaging to enhance the care, well-being and experimental outcomes of laboratory non-human primates (monkeys)

Over the past 10-20 years, neuroscience witnessed an explosion in the use of non-invasive imaging methods, particularly magnetic resonance imaging (MRI), to study brain structure and function. Simultaneously, with access to MRI in many research institutions, MRI has become an indispensable tool for researchers and veterinarians to guide improvements in surgical procedures and implants and thus, experimental as well as clinical outcomes, given that access to MRI also allows for improved diagnosis and monitoring for brain disease. As part of the PRIMEatE Data Exchange, we gathered expert scientists, veterinarians, and clinicians who treat humans, to provide an overview of the use of non-invasive imaging tools, primarily MRI, to enhance experimental and welfare outcomes for laboratory non-human primates engaged in neuroscientific experiments. We aimed to provide guidance for other researchers, scientists and veterinarians in the use of this powerful imaging technology as well as to foster a larger conversation and community of scientists and veterinarians with a shared goal of improving the well-being and experimental outcomes for laboratory animals.

Variability in atlas registration of optical intrinsic signal imaging and its effect on functional connectivity analysis

To compare neuroimaging data between subjects, images from individual sessions need to be aligned to a common reference or "atlas." Atlas registration of optical intrinsic signal imaging of mice, for example, is commonly performed using affine transforms with parameters determined by manual selection of canonical skull landmarks. Errors introduced by such procedures have not previously been investigated. We quantify the variability that arises from this process and consequent errors from misalignment that affect interpretation of functional neuroimaging data. We propose an improved method, using separately acquired high-resolution images and demonstrate improvements in variability and alignment using this method.

Normative Analysis of Individual Brain Differences Based on a Population MRI-Based Atlas of Cynomolgus Macaques

The developmental trajectory of the primate brain varies substantially with aging across subjects. However, this ubiquitous variability between individuals in brain structure is difficult to quantify and has thus essentially been ignored. Based on a large-scale structural magnetic resonance imaging dataset acquired from 162 cynomolgus macaques, we create a species-specific 3D template atlas of the macaque brain, and deploy normative modeling to characterize individual variations of cortical thickness (CT) and regional gray matter volume (GMV). We observed an overall decrease in total GMV and mean CT, and an increase in white matter volume from juvenile to early adult. Specifically, CT and regional GMV were greater in prefrontal and temporal cortices relative to early unimodal areas. Age-dependent trajectories of thickness and volume for each cortical region revealed an increase in the medial temporal lobe, and decreases in all other regions. A low percentage of highly individualized deviations of CT and GMV were identified (0.0021%, 0.0043%, respectively, P < 0.05, false discovery rate [FDR]-corrected). Our approach provides a natural framework to parse individual neuroanatomical differences for use as a reference standard in macaque brain research, potentially enabling inferences regarding the degree to which behavioral or symptomatic variables map onto brain structure in future disease studies.

Pharmacokinetic Modeling of (R)-[11C]verapamil to Measure the P-Glycoprotein Function in Nonhuman Primates

(R)-[¹¹C]verapamil is a radiotracer widely used for the evaluation of the P-glycoprotein (P-gp) function at the blood–brain barrier (BBB). Several studies have evaluated the pharmacokinetics of (R)-[¹¹C]verapamil in rats and humans under different conditions. However, to the best of our knowledge, the pharmacokinetics of (R)-[¹¹C]verapamil have not yet been evaluated in nonhuman primates. Our study aims to establish (R)-[¹¹C]verapamil as a reference P-gp tracer for comparison of a newly developed P-gp positron emission tomography (PET) tracer in a species close to humans. Therefore, the study assesses the kinetics of (R)-[¹¹C]verapamil and evaluates the effect of scan duration and P-gp inhibition on estimated pharmacokinetic parameters. Three nonhuman primates underwent two dynamic 91 min PET scans with arterial blood sampling, one at baseline and another after inhibition of the P-gp function. The (R)-[¹¹C]verapamil data were analyzed using 1-tissue compartment model (1-TCM) and 2-tissue compartment model fits using plasma-corrected for polar radio-metabolites or non-corrected for radio-metabolites as an input function and with various scan durations (10, 20, 30, 60, and 91 min). The preferred model was chosen according to the Akaike information criterion and the standard errors (SE %) of the estimated parameters. 1-TCM was selected as the model of choice to analyze the (R)-[¹¹C]verapamil data at baseline and after inhibition and for all scan durations tested. The volume of distribution (V_T) and the efflux constant k₂ estimations were affected by the evaluated scan durations, whereas the influx constant K₁ estimations remained relatively constant. After P-gp inhibition (tariquidar, 8 mg/kg), in a 91 min scan duration, the whole-brain V_T increased significantly up to 208% (p < 0.001) and K₁ up to 159% (p < 0.001) compared with baseline scans. The k₂ values decreased significantly after P-gp inhibition in all the scan durations except for the 91 min scans. This study suggests the use of K₁, calculated with 1-TCM and using short PET scans (10 to 30 min), as a suitable parameter to measure the P-gp function at the BBB of nonhuman primates.

A collaborative resource platform for non-human primate neuroimaging

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.

In vivo Population Averaged Stereotaxic T2w MRI Brain Template for the Adult Yucatan Micropig

Population averaged brain templates are an essential tool for imaging-based neuroscience research, providing investigators with information about the expected size and morphology of brain structures and the spatial relationships between them, within a demographic cross-section. This allows for a standardized comparison of neuroimaging data between subjects and provides neuroimaging software with a probabilistic framework upon which further processing and analysis can be based. Many different templates have been created to represent specific study populations and made publicly available for human and animal research. An increasingly studied animal model in the neurosciences that still lacks appropriate brain templates is the adult Yucatan micropig. In particular, T2-weighted templates are absent in this species as a whole. To address this need and provide a tool for neuroscientists wishing to pursue neuroimaging research in the adult micropig, we present the construction of population averaged (n = 16) T2-weighted MRI brain template for the adult Yucatan micropig. Additionally, we present initial analysis of T1-weighted (n = 3), and diffusion-weighted (n = 3) images through multimodal registration of these contrasts to our T2 template. The strategies used here may also be generalized to create similar templates for other study populations or species in need of template construction.

Signature of consciousness in brain-wide synchronization patterns of monkey and human fMRI signals

During the sleep-wake cycle, the brain undergoes profound dynamical changes, which manifest subjectively as transitions between conscious experience and unconsciousness. Yet, neurophysiological signatures that can objectively distinguish different consciousness states based are scarce. Here, we show that differences in the level of brain-wide signals can reliably distinguish different stages of sleep and anesthesia from the awake state in human and monkey fMRI resting state data. Moreover, a whole-brain computational model can faithfully reproduce changes in global synchronization and other metrics such as functional connectivity, structure-function relationship, integration and segregation across vigilance states. We demonstrate that the awake brain is close to a Hopf bifurcation, which naturally coincides with the emergence of globally correlated fMRI signals. Furthermore, simulating lesions of individual brain areas highlights the importance of connectivity hubs in the posterior brain and subcortical nuclei for maintaining the model in the awake state, as predicted by graph-theoretical analyses of structural data.

The macaque brain ONPRC18 template with combined gray and white matter labelmap for multimodal neuroimaging studies of Nonhuman Primates

Macaques are the most common nonhuman primate (NHP) species used in neuroscience research. With the advancement of many neuroimaging techniques, new studies are beginning to apply multiple types of in vivo mag netic resonance imaging (MRI), such as structural imaging (sMRI) with T1 and T2 weighted contrasts alongside diffusion weighed (DW) imaging. In studies involving rhesus macaques, this approach can be used to better under stand micro-structural changes that occur during development, in various disease states or with normative aging. However, many of the available rhesus brain atlases have been designed for only one imaging modality, making it difficult to consistently define the same brain regions across multiple imaging modalities in the same subject. To address this, we created a brain atlas from 18 adult rhesus macaques that includes co-registered templates constructed from images frequently used to characterize macroscopic brain structure (T2/SPACE and T1/MP-RAGE), and a diffusion tensor imaging (DTI) template. The DTI template was up-sampled from 1 mm isotropic resolution to resolution match to the T1 and T2-weighted images (0.5 mm isotropic), and the parameter maps were derived for FA, AD, RD and MD. The labelmap volumes delineate 57 gray matter regions of interest (ROIs; 36 cortical regions and 21 subcortical structures), as well as 74 white matter tracts. Importantly, the labelmap overlays both the structural and diffusion templates, enabling the same regions to be consistently identified across imaging modalities. A specialized condensed version of the labelmap ROIs are also included to further extend the usefulness of this tool for imaging data with lower spatial resolution, such as functional MRI (fMRI) or positron emission tomography (PET).

Visual and Vestibular Selectivity for Self-Motion in Macaque Posterior Parietal Area 7a

We examined the responses of neurons in posterior parietal area 7a to passive rotational and translational self-motion stimuli, while systematically varying the speed of visually simulated (optic flow cues) or actual (vestibular cues) self-motion. Contrary to a general belief that responses in area 7a are predominantly visual, we found evidence for a vestibular dominance in self-motion processing. Only a small fraction of neurons showed multisensory convergence of visual/vestibular and linear/angular self-motion cues. These findings suggest possibly independent neuronal population codes for visual versus vestibular and linear versus angular self-motion. Neural responses scaled with self-motion magnitude (i.e., speed) but temporal dynamics were diverse across the population. Analyses of laminar recordings showed a strong distance-dependent decrease for correlations in stimulus-induced (signal correlation) and stimulus-independent (noise correlation) components of spike-count variability, supporting the notion that neurons are spatially clustered with respect to their sensory representation of motion. Single-unit and multiunit response patterns were also correlated, but no other systematic dependencies on cortical layers or columns were observed. These findings describe a likely independent multimodal neural code for linear and angular self-motion in a posterior parietal area of the macaque brain that is connected to the hippocampal formation.

Pharmacokinetic Modeling of [18F]MC225 for Quantification of the P-Glycoprotein Function at the Blood-Brain Barrier in Non-Human Primates with PET

[¹⁸F]MC225 has been developed as a weak substrate of P-glycoprotein (P-gp) aimed to measure changes in the P-gp function at the blood–brain barrier with positron emission tomography. This study evaluates [¹⁸F]MC225 kinetics in non-human primates and investigates the effect of both scan duration and P-gp inhibition. Three rhesus monkeys underwent two 91-min dynamic scans with blood sampling at baseline and after P-gp inhibition (8 mg/kg tariquidar). Data were analyzed using the 1-tissue compartment model (1-TCM) and 2-tissue compartment model (2-TCM) fits using metabolite-corrected plasma as the input function and for various scan durations (10, 20, 30, 60, and 91 min). The preferred model was chosen according to the Akaike information criterion and the standard errors (%) of the estimated parameters. For the 91-min scan duration, the influx constant K₁ increased by 40.7% and the volume of distribution (V_T) by 30.4% after P-gp inhibition, while the efflux constant k₂ did not change significantly. Similar changes were found for all evaluated scan durations. K₁ did not depend on scan duration (10 min—K₁ = 0.2191 vs 91 min—K₁ = 0.2258), while V_T and k₂ did. A scan duration of 10 min seems sufficient to properly evaluate the P-gp function using K₁ obtained with 1-TCM. For the 91-min scan, V_T and K₁ can be estimated with a 2-TCM, and both parameters can be used to assess P-gp function.

A Causal Network Analysis of Neuromodulation in the Mood Processing Network

Neural decoding and neuromodulation technologies hold great promise for treating mood and other brain disorders in next-generation therapies that manipulate functional brain networks. Here we perform a novel causal network analysis to decode multiregional communication in the primate mood processing network and determine how neuromodulation, short-burst tetanic microstimulation (sbTetMS), alters multiregional network communication. The causal network analysis revealed a mechanism of network excitability that regulates when a sender stimulation site communicates with receiver sites. Decoding network excitability from neural activity at modulator sites predicted sender-receiver communication, whereas sbTetMS neuromodulation temporarily disrupted sender-receiver communication. These results reveal specific network mechanisms of multiregional communication and suggest a new generation of brain therapies that combine neural decoding to predict multiregional communication with neuromodulation to disrupt multiregional communication.

Behavioral flexibility is associated with changes in structure and function distributed across a frontal cortical network in macaques

One of the most influential accounts of central orbitofrontal cortex-that it mediates behavioral flexibility-has been challenged by the finding that discrimination reversal in macaques, the classic test of behavioral flexibility, is unaffected when lesions are made by excitotoxin injection rather than aspiration. This suggests that the critical brain circuit mediating behavioral flexibility in reversal tasks lies beyond the central orbitofrontal cortex. To determine its identity, a group of nine macaques were taught discrimination reversal learning tasks, and its impact on gray matter was measured. Magnetic resonance imaging scans were taken before and after learning and compared with scans from two control groups, each comprising 10 animals. One control group learned discrimination tasks that were similar but lacked any reversal component, and the other control group engaged in no learning. Gray matter changes were prominent in posterior orbitofrontal cortex/anterior insula but were also found in three other frontal cortical regions: lateral orbitofrontal cortex (orbital part of area 12 [12o]), cingulate cortex, and lateral prefrontal cortex. In a second analysis, neural activity in posterior orbitofrontal cortex/anterior insula was measured at rest, and its pattern of coupling with the other frontal cortical regions was assessed. Activity coupling increased significantly in the reversal learning group in comparison with controls. In a final set of experiments, we used similar structural imaging procedures and analyses to demonstrate that aspiration lesion of central orbitofrontal cortex, of the type known to affect discrimination learning, affected structure and activity in the same frontal cortical circuit. The results identify a distributed frontal cortical circuit associated with behavioral flexibility.

A population stereotaxic positron emission tomography brain template for the macaque and its application to ischemic model

PURPOSE

Positron emission tomography (PET) is a non-invasive imaging tool for the evaluation of brain function and neuronal activity in normal and diseased conditions with high sensitivity. The macaque monkey serves as a valuable model system in the field of translational medicine, for its phylogenetic proximity to man. To translation of non-human primate neuro-PET studies, an effective and objective data analysis platform for neuro-PET studies is needed.

MATERIALS AND METHODS

A set of stereotaxic templates of macaque brain, namely the Institute of High Energy Physics & Jinan University Macaque Template (HJT), was constructed by iteratively registration and averaging, based on 30 healthy rhesus monkeys. A brain atlas image was created in HJT space by combining sub-anatomical regions and defining new 88 bilateral functional regions, in which a unique integer was assigned for each sub-anatomical region.

RESULTS

The HJT comprised a structural MRI T1 weighted image (T1WI) template image, a functional FDG-PET template image, intracranial tissue segmentations accompanied with a digital macaque brain atlas image. It is compatible with various commercially available software tools, such as SPM and PMOD. Data analysis was performed on a stroke model compared with a group of healthy controls to demonstrate the usage of HJT.

CONCLUSION

We have constructed a stereotaxic template set of macaque brain named HJT, which standardizes macaque neuroimaging data analysis, supports novel radiotracer development and facilitates translational neuro-disorders research.

Large-scale comparative neuroimaging: Where are we and what do we need?

Neuroimaging has a lot to offer comparative neuroscience. Although invasive "gold standard" techniques have a better spatial resolution, neuroimaging allows fast, whole-brain, repeatable, and multi-modal measurements of structure and function in living animals and post-mortem tissue. In the past years, comparative neuroimaging has increased in popularity. However, we argue that its most significant potential lies in its ability to collect large-scale datasets of many species to investigate principles of variability in brain organisation across whole orders of species-an ambition that is presently unfulfilled but achievable. We briefly review the current state of the field and explore what the current obstacles to such an approach are. We propose some calls to action.

Rhesus Macaque Brain Atlas Regions Aligned to an MRI Template

To aid in the analysis of rhesus macaque brain images, we aligned digitized anatomical regions from the widely used atlas of Paxinos et al. to a published magnetic resonance imaging (MRI) template based on a large number of subjects. Digitally labelled atlas images were aligned to the template in 2D and then in 3D. The resulting grey matter regions appear qualitatively to be well registered to the template. To quantitatively validate the procedure, MR brain images of 20 rhesus macaques were aligned to the template along with regions drawn by hand in striatal and cortical areas in each subject's MRI. There was good geometric overlap between the hand drawn regions and the template regions. Positron emission tomography (PET) images of the same subjects showing uptake of a dopamine D₂ receptor ligand were aligned to the template space, and good agreement was found between tracer binding measures calculated using the hand drawn and template regions. In conclusion, an anatomically defined set of rhesus macaque brain regions has been aligned to an MRI template and has been validated for analysis of PET imaging in a subset of striatal and cortical areas. The entire set of over 200 regions is publicly available at https://www.nitrc.org/ . Graphical Abstract ᅟ.

A Web-Based Atlas Combining MRI and Histology of the Squirrel Monkey Brain

The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI and histological atlases serve as valuable resources for anatomical, physiological, and functional studies of the brain; however, no digital MRI/histology atlas is currently available for the squirrel monkey. This paper describes the construction of a web-based multi-modal atlas of the squirrel monkey brain. The MRI-derived information includes anatomical MRI contrast (i.e., T2-weighted and proton-density-weighted) and diffusion MRI metrics (i.e., fractional anisotropy and mean diffusivity) from data acquired both in vivo and ex vivo on a 9.4 Tesla scanner. The histological images include Nissl and myelin stains, co-registered to the corresponding MRI, allowing identification of cyto- and myelo-architecture. In addition, a bidirectional neuronal tracer, biotinylated dextran amine (BDA) was injected into the primary motor cortex, enabling highly specific identification of regions connected to the injection location. The atlas integrates the results of common image analysis methods including diffusion tensor imaging glyphs, labels of 57 white-matter tracts identified using DTI-tractography, and 18 cortical regions of interest identified from Nissl-revealed cyto-architecture. All data are presented in a common space, and all image types are accessible through a web-based atlas viewer, which allows visualization and interaction of user-selectable contrasts and varying resolutions. By providing an easy to use reference system of anatomical information, our web-accessible multi-contrast atlas forms a rich and convenient resource for comparisons of brain findings across subjects or modalities. The atlas is called the Combined Histology-MRI Integrated Atlas of the Squirrel Monkey (CHIASM). All images are accessible through our web-based viewer ( https://chiasm.vuse.vanderbilt.edu /), and data are available for download at ( https://www.nitrc.org/projects/smatlas/ ).

Sulcal organization in the medial frontal cortex provides insights into primate brain evolution

Although the relative expansion of the frontal cortex in primate evolution is generally accepted, the nature of the human uniqueness, if any, and between-species anatomo-functional comparisons of the frontal areas remain controversial. To provide a novel interpretation of the evolution of primate brains, sulcal morphological variability of the medial frontal cortex was assessed in Old World monkeys (macaque/baboon) and Hominoidea (chimpanzee/human). We show that both Hominoidea possess a paracingulate sulcus, which was previously thought to be unique to the human brain and linked to higher cognitive functions, such as mentalizing. Also, we show systematic sulcal morphological organization of the medial frontal cortex that can be traced from Old World monkeys to Hominoidea species, demonstrating an evolutionarily conserved organizational principle. These data provide a new framework to compare sulcal morphology, cytoarchitectonic areal distribution, connectivity, and function across the primate order, leading to clear predictions about how other primate brains might be anatomo-functionally organized.

Fine-Grained Parcellation of the Macaque Nucleus Accumbens by High-Resolution Diffusion Tensor Tractography

Limited in part by the spatial resolution of typical in vivo magnetic resonance imaging (MRI) data, recent neuroimaging studies have only identified a connectivity-based shell-core-like partitioning of the nucleus accumbens (Acb) in humans. This has hindered the process of making a more refined description of the Acb using non-invasive neuroimaging technologies and approaches. In this study, high-resolution ex vivo macaque brain diffusion MRI data were acquired to investigate the tractography-based parcellation of the Acb. Our results identified a shell-core-like partitioning in macaques that is similar to that in humans as well as an alternative solution that subdivided the Acb into four parcels, the medial shell, the lateral shell, the ventral core, and the dorsal core. Furthermore, we characterized the specific anatomical and functional connectivity profiles of these Acb subregions and generalized their specialized functions to establish a fine-grained macaque Acb brainnetome atlas. This atlas should be helpful in neuroimaging, stereotactic surgery, and comparative neuroimaging studies to reveal the neurophysiological substrates of various diseases and cognitive functions associated with the Acb.

Interspecies Differences in the Connectivity of Ventral Striatal Components Between Humans and Macaques

Although the evolutionarily conserved functions of the ventral striatal components have been used as a priori knowledge for further study, whether these functions are conserved between species remains unclear. In particular, whether macroscopic connectivity supports this given the disproportionate volumetric differences between species in the brain regions that project to the ventral striatum, including the prefrontal and limbic areas, has not been established In this study, the human and macaque striatum was first tractographically parcellated to define the ventral striatum and its two subregions, the nucleus accumbens (Acb)-like and the neurochemically unique domains of the Acb and putamen (NUDAPs)-like divisions. Our results revealed a similar topographical distribution of the connectivity-based ventral striatal components in the two primate brains. Successively, a set of targets was extracted to construct a connectivity fingerprint to characterize these parcellation results, enabling cross-species comparisons. Our results indicated that the connectivity fingerprints of the ventral striatum-like divisions were dissimilar in the two species. We localized this difference to specific targets to analyze possible interspecies functional modifications. Our results also revealed interspecies-convergent connectivity ratio fingerprints of the target group to these two ventral striatum-like subregions. This convergence may suggest synchronous connectional changes of these ventral striatal components during primate evolution.

Rise of the Visible Monkey: Sectioned Images of Rhesus Monkey

BACKGROUND

Gross anatomy and sectional anatomy of a monkey should be known by students and researchers of veterinary medicine and medical research. However, materials to learn the anatomy of a monkey are scarce. Thus, the objective of this study was to produce a Visible Monkey data set containing cross sectional images, computed tomographs (CTs), and magnetic resonance images (MRIs) of a monkey whole body.

METHODS

Before and after sacrifice, a female rhesus monkey was used for 3 Tesla MRI and CT scanning. The monkey was frozen and sectioned at 0.05 mm intervals for the head region and at 0.5 mm intervals for the rest of the body using a cryomacrotome. Each sectioned surface was photographed using a digital camera to obtain horizontal sectioned images. Segmentation of sectioned images was performed to elaborate three-dimensional (3D) models of the skin and brain.

RESULTS

A total of 1,612 horizontal sectioned images of the head and 1,355 images of the remaining region were obtained. The small pixel size (0.024 mm × 0.024 mm) and real color (48 bits color) of these images enabled observations of minute structures.

CONCLUSION

Due to small intervals of these images, continuous structures could be traced completely. Moreover, 3D models of the skin and brain could be used for virtual dissections. Sectioned images of this study will enhance the understanding of monkey anatomy and foster further studies. These images will be provided to any requesting researcher free of charge.

Macro-connectomics and microstructure predict dynamic plasticity patterns in the non-human primate brain

The brain displays a remarkable ability to adapt following injury by altering its connections through neural plasticity. Many of the biological mechanisms that underlie plasticity are known, but there is little knowledge as to when, or where in the brain plasticity will occur following injury. This knowledge could guide plasticity-promoting interventions and create a more accurate roadmap of the recovery process following injury. We causally investigated the time-course of plasticity after hippocampal lesions using multi-modal MRI in monkeys. We show that post-injury plasticity is highly dynamic, but also largely predictable on the basis of the functional connectivity of the lesioned region, gradients of cell densities across the cortex and the pre-lesion network structure of the brain. The ability to predict which brain areas will plastically adapt their functional connectivity following injury may allow us to decipher why some brain lesions lead to permanent loss of cognitive function, while others do not.

The brain has the ability to adapt after injury, a process known as plasticity. When one area sustains damage, for example following a car accident or stroke, other areas change their activity and structure to compensate. Understanding how this happens is critical to helping people recover from brain injuries. Certain factors may affect how well the brain can repair itself. These include how much the damaged area interacts with other areas, and which cell types different areas of the brain contain.

Froudist-Walsh et al. set out to determine how these factors influence recovery from brain injury in monkeys, whose brains are similar to our own. The monkeys had damage to a structure called the hippocampus. This part of the brain has a key role in memory, which is often impaired in patients with brain injuries. The hippocampus cannot repair itself because the brain has only a limited capacity to grow new neurons. Instead, the brain attempts to compensate for disruption to the hippocampus via changes in other, undamaged areas.

Using brain imaging, Froudist-Walsh et al. show that the types of changes that occur depend on how much time has passed since the injury. In the first three months, many areas of the brain change how much they coordinate their activity with other areas. Highly connected areas reduce their communication with other areas the most. In the long-term, the responses of brain areas depend more on which cell types they contain. Areas with more support cells known as “glia” – which supply nutrients and energy to neurons – are better able to adapt their connectivity up to a year after the injury.

These findings may ultimately benefit people who have suffered brain injuries after accidents or stroke. They suggest that stimulating intact brain areas may be helpful in the months immediately after an injury. By contrast, long-term therapy may need to focus more on structural repair. Future studies must build on these results to discover the best ways to induce successful recovery from brain injury.