Surface-based and probabilistic atlases of primate cerebral cortex

Functional connectivity of the macaque posterior parahippocampal cortex

Neuroimaging experiments in humans suggest that regions in parietal cortex and along the posterior midline are functionally connected to the medial temporal lobe and are active during memory retrieval. It is unknown whether macaques have a similar network. We examined functional connectivity in isoflurane-anesthetized macaques to identify a network associated with posterior parahippocampal cortex (PPHC). Functional connectivity was observed between the PPHC and retrosplenial, posterior cingulate, superior temporal gyrus, and inferior parietal cortex. PPHC correlations were distinct from regions in parietal and temporal cortex activated by an oculomotor task. Comparison of macaque and human PPHC correlations revealed similarities that suggest the temporal-parietal region identified in the macaque may share a common lineage with human Brodmann area 39, a region thought to be involved in recollection. These results suggest that macaques and humans may have homologous PPHC-parietal pathways. By specifying the location of the putative macaque homologue in parietal cortex, we provide a target for future physiological exploration of this area's role in mnemonic or alternative processes.

Rhesus macaque brain morphometry: a methodological comparison of voxel-wise approaches

Voxel-based morphometry studies have become increasingly common in human neuroimaging over the past several years; however, few studies have utilized this method to study morphometry changes in non-human primates. Here we describe the application of voxel-wise morphometry methods to the rhesus macaque (Macaca mulatta) using the 112RM-SL template and priors (McLaren et al. (2009) [42]) and as an illustrative example we describe age-associated changes in grey matter morphometry. Specifically, we evaluated the unified segmentation routine implemented using Statistical Parametric Mapping (SPM) software and the FMRIB's Automated Segmentation Tool (FAST) in the FMRIB Software Library (FSL); the effect of varying the smoothing kernel; and the effect of the normalization routine. We found that when studying non-human primates, brain images need less smoothing than in human studies, 2-4mm FWHM. Using flow field deformations (DARTEL) improved inter-subject alignment leading to results that were more likely due to morphometry differences as opposed to registration differences.

Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex

The Allen Brain Atlas (ABA, www.brain-map.org) is a genome wide, spatially registered collection of cellular resolution in situ hybridization gene expression image data of the C57Bl/6J mouse brain. Derived from the ABA, the Anatomic Gene Expression Atlas (AGEA, http://mouse.brain-map.org/agea) has demonstrated both laminar and areal spatial gene expression correlations in the mouse cortex. While the mouse cortex is lissencephalic, its curvature and substantial bending in boundary areas renders it difficult to visualize and analyze laminar versus areal effects in a rectilinear coordinate framework. In context of human and non-human primate cortex, surface-based representation has proven useful for understanding relative locations of laminar, columnar, and areal features. In this paper, we describe a methodology for constructing surface-based flatmaps of the mouse cortex that enables mapping of gene expression data from individual genes in the ABA, or probabilistic expression maps from the AGEA, to identify and visualize genetic relationships between layers and areas.

The brain atlas concordance problem: quantitative comparison of anatomical parcellations

Many neuroscientific reports reference discrete macro-anatomical regions of the brain which were delineated according to a brain atlas or parcellation protocol. Currently, however, no widely accepted standards exist for partitioning the cortex and subcortical structures, or for assigning labels to the resulting regions, and many procedures are being actively used. Previous attempts to reconcile neuroanatomical nomenclatures have been largely qualitative, focusing on the development of thesauri or simple semantic mappings between terms. Here we take a fundamentally different approach, discounting the names of regions and instead comparing their definitions as spatial entities in an effort to provide more precise quantitative mappings between anatomical entities as defined by different atlases. We develop an analytical framework for studying this brain atlas concordance problem, and apply these methods in a comparison of eight diverse labeling methods used by the neuroimaging community. These analyses result in conditional probabilities that enable mapping between regions across atlases, which also form the input to graph-based methods for extracting higher-order relationships between sets of regions and to procedures for assessing the global similarity between different parcellations of the same brain. At a global scale, the overall results demonstrate a considerable lack of concordance between available parcellation schemes, falling within chance levels for some atlas pairs. At a finer level, this study reveals spatial relationships between sets of defined regions that are not obviously apparent; these are of high potential interest to researchers faced with the challenge of comparing results that were based on these different anatomical models, particularly when coordinate-based data are not available. The complexity of the spatial overlap patterns revealed points to problems for attempts to reconcile anatomical parcellations and nomenclatures using strictly qualitative and/or categorical methods. Detailed results from this study are made available via an interactive web site at http://obart.info.

Multisensory functional magnetic resonance imaging: a future perspective

Advances in functional magnetic resonance imaging (fMRI) technology and analytic tools provide a powerful approach to unravel how the human brain combines the different sensory systems. In this perspective, we outline promising future directions of fMRI to make optimal use of its strengths in multisensory research, and to meet its weaker sides by combining it with other imaging modalities and computational modeling.

Computational morphometry for detecting changes in brain structure due to development, aging, learning, disease and evolution

The brain, like any living tissue, is constantly changing in response to genetic and environmental cues and their interaction, leading to changes in brain function and structure, many of which are now in reach of neuroimaging techniques. Computational morphometry on the basis of Magnetic Resonance (MR) images has become the method of choice for studying macroscopic changes of brain structure across time scales. Thanks to computational advances and sophisticated study designs, both the minimal extent of change necessary for detection and, consequently, the minimal periods over which such changes can be detected have been reduced considerably during the last few years. On the other hand, the growing availability of MR images of more and more diverse brain populations also allows more detailed inferences about brain changes that occur over larger time scales, way beyond the duration of an average research project. On this basis, a whole range of issues concerning the structures and functions of the brain are now becoming addressable, thereby providing ample challenges and opportunities for further contributions from neuroinformatics to our understanding of the brain and how it changes over a lifetime and in the course of evolution.

Paracingulate asymmetry in anterior and midcingulate cortex: sex differences and the effect of measurement technique

Many structural brain asymmetries accompany left hemisphere language dominance. For example, the cingulate sulcus is larger in the medial cortex of the right hemisphere, while the more dorsal paracingulate sulcus is larger on the left. The functional significance of these asymmetries is unknown because fMRI studies rarely attempt to localize activation to specific sulci, possibly due to difficulties in consistent sulcal identification. In medial cortex, for example, there are many regions of partial sulcal overlap where MRI images do not provide sufficient information to unambiguously distinguish a paracingulate sulcus from a displaced anterior cingulate segment. As large samples of postmortem material are rarely available for cytoarchitectural studies of sulcal variation, we have investigated the effect of variation in boundary and sulcal definition on paracingulate asymmetry in the MRI scans of 200 healthy adults (100 men, 100 women). Although women displayed a reliable asymmetry in the size of the paracingulate sulcus, regardless of boundary definition or technique, asymmetry was greatest when (1) the measurement was limited to the midcingulate region between the genu and the anterior commissure; and (2) the more dorsal of two overlapping sulci was always classified as a paracingulate sulcus (rather than as a displaced cingulate segment). The fact that paracingulate asymmetry is maximal in the midcingulate region suggests that this region may play a particular role in hemispheric specialization for language. Future work should investigate the structural and functional correlates of sulcal variation in this region.

Visualizing data mining results with the brede tools

A few neuroinformatics databases now exist that record results from neuroimaging studies in the form of brain coordinates in stereotaxic space. The Brede Toolbox was originally developed to extract, analyze and visualize data from one of them - the BrainMap database. Since then the Brede Toolbox has expanded and now includes its own database with coordinates along with ontologies for brain regions and functions: The Brede Database. With Brede Toolbox and Database combined, we setup automated workflows for extraction of data, mass meta-analytic data mining and visualizations. Most of the Web presence of the Brede Database is established by a single script executing a workflow involving these steps together with a final generation of Web pages with embedded visualizations and links to interactive three-dimensional models in the Virtual Reality Modeling Language. Apart from the Brede tools I briefly review alternate visualization tools and methods for Internet-based visualization and information visualization as well as portals for visualization tools.

Lost in localization--but found with foci?!

Commentaries by Derrfuss and Mar [Derrfuss, J., Mar, R.A., 2009. Lost in localization: the need for a universal coordinate database. Neuroimage (doi:10.1016/j.neuroimage.2009.01.053).], Nielsen [Nielsen, F.A., 2009. Lost in localization: a solution with neuroinformatics 2.0? Neuroimage.], Hamilton [Hamilton, A., 2009. Lost in localization: a minimal middle way. Neuroimage.], and Laird and Fox [Laird, A.R., Fox, P.T., 2009 Lost in localization? The focus is meta-analysis. Neuroimage.] agree on the need for a comprehensive database of published stereotaxic coordinates but offer diverse views on how best to achieve this objective. Here, I summarize recent enhancements to the SumsDB database that increase its utility and decrease the impediments to data submission, thereby making it attractive as a resource that can approach comprehensive content in a realistic time frame.

Matching categorical object representations in inferior temporal cortex of man and monkey

Inferior temporal (IT) object representations have been intensively studied in monkeys and humans, but representations of the same particular objects have never been compared between the species. Moreover, IT's role in categorization is not well understood. Here, we presented monkeys and humans with the same images of real-world objects and measured the IT response pattern elicited by each image. In order to relate the representations between the species and to computational models, we compare response-pattern dissimilarity matrices. IT response patterns form category clusters, which match between man and monkey. The clusters correspond to animate and inanimate objects; within the animate objects, faces and bodies form subclusters. Within each category, IT distinguishes individual exemplars, and the within-category exemplar similarities also match between the species. Our findings suggest that primate IT across species may host a common code, which combines a categorical and a continuous representation of objects.

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

Posterior parietal cortex and episodic encoding: insights from fMRI subsequent memory effects and dual-attention theory

The formation of episodic memories--memories for life events--is affected by attention during event processing. A leading neurobiological model of attention posits two separate yet interacting systems that depend on distinct regions in lateral posterior parietal cortex (PPC). From this dual-attention perspective, dorsal PPC is thought to support the goal-directed allocation of attention, whereas ventral PPC is thought to support reflexive orienting to information that automatically captures attention. To advance understanding of how parietal mechanisms may impact event encoding, we review functional MRI studies that document the relationship between lateral PPC activation during encoding and subsequent memory performance (e.g., later remembering or forgetting). This review reveals that (a) encoding-related activity is frequently observed in human lateral PPC, (b) increased activation in dorsal PPC is associated with later memory success, and (c) increased activation in ventral PPC predominantly correlates with later memory failure. From a dual-attention perspective, these findings suggest that allocating goal-directed attention during event processing increases the probability that the event will be remembered later, whereas the capture of reflexive attention during event processing may have negative consequences for event encoding. The prevalence of encoding-related activation in parietal cortex suggests that neurobiological models of episodic memory should consider how parietal-mediated attentional mechanisms regulate encoding.

Matching spatial with ontological brain regions using Java tools for visualization, database access, and integrated data analysis

Brain atlases are widely used in experimental neuroscience as tools for locating and targeting specific brain structures. Delineated structures in a given atlas, however, are often difficult to interpret and to interface with database systems that supply additional information using hierarchically organized vocabularies (ontologies). Here we discuss the concept of volume-to-ontology mapping in the context of macroscopical brain structures. We present Java tools with which we have implemented this concept for retrieval of mapping and connectivity data on the macaque brain from the CoCoMac database in connection with an electronic version of "The Rhesus Monkey Brain in Stereotaxic Coordinates" authored by George Paxinos and colleagues. The software, including our manually drawn monkey brain template, can be downloaded freely under the GNU General Public License. It adds value to the printed atlas and has a wider (neuro-)informatics application since it can read appropriately annotated data from delineated sections of other species and organs, and turn them into 3D registered stacks. The tools provide additional features, including visualization and analysis of connectivity data, volume and centre-of-mass estimates, and graphical manipulation of entire structures, which are potentially useful for a range of research and teaching applications.

Multiple parietal operculum subdivisions in humans: tactile activation maps

We focused the present analysis on blood-oxygen-level-dependent responses evoked in four architectonic subdivisions of human posterior parietal operculum (PO) during two groups of tasks involving either vibrotactile stimulation or rubbing different surfaces against the right index finger pad. Activity localized in previously defined parietal opercular subdivisions, OP 1-4, was co-registered to a standard cortical surface-based atlas. Four vibrotactile stimulation tasks involved attention to the parameters of paired vibrations: (1) detect rare target trials when vibration frequencies matched; (2) select the presentation order of the vibration with a higher frequency or (3) longer duration; and (4) divide attention between frequency and duration before selecting stimulus order. Surface stimulation tasks involved various discriminations of different surfaces: (1) smooth surfaces required no discrimination; (2) paired horizontal gratings required determination of the direction of roughness change; (3) paired shapes entailed identifying matched and unmatched shapes; (4) raised letters involved letter recognition. The results showed activity in multiple somatosensory subdivisions bilaterally in human PO that are plausibly homologues of somatosensory areas previously described in animals. All tasks activated OP 1, but in vibrotactile tasks foci were more restricted compared to moving surface tasks. Greater spatial extents of activity especially in OP 1 and 4 when surfaces rubbed the finger pad did not support previously reported somatotopy of the second finger representation in "S2". The varied activity distributions across OP subdivisions may reflect low-level perceptual and/or cognitive processing differences between tasks.

In vivo assessment of cold adaptation in insect larvae by magnetic resonance imaging and magnetic resonance spectroscopy

BACKGROUND

Temperatures below the freezing point of water and the ensuing ice crystal formation pose serious challenges to cell structure and function. Consequently, species living in seasonally cold environments have evolved a multitude of strategies to reorganize their cellular architecture and metabolism, and the underlying mechanisms are crucial to our understanding of life. In multicellular organisms, and poikilotherm animals in particular, our knowledge about these processes is almost exclusively due to invasive studies, thereby limiting the range of conclusions that can be drawn about intact living systems.

METHODOLOGY

Given that non-destructive techniques like (1)H Magnetic Resonance (MR) imaging and spectroscopy have proven useful for in vivo investigations of a wide range of biological systems, we aimed at evaluating their potential to observe cold adaptations in living insect larvae. Specifically, we chose two cold-hardy insect species that frequently serve as cryobiological model systems--the freeze-avoiding gall moth Epiblema scudderiana and the freeze-tolerant gall fly Eurosta solidaginis.

RESULTS

In vivo MR images were acquired from autumn-collected larvae at temperatures between 0 degrees C and about -70 degrees C and at spatial resolutions down to 27 microm. These images revealed three-dimensional (3D) larval anatomy at a level of detail currently not in reach of other in vivo techniques. Furthermore, they allowed visualization of the 3D distribution of the remaining liquid water and of the endogenous cryoprotectants at subzero temperatures, and temperature-weighted images of these distributions could be derived. Finally, individual fat body cells and their nuclei could be identified in intact frozen Eurosta larvae.

CONCLUSIONS

These findings suggest that high resolution MR techniques provide for interesting methodological options in comparative cryobiological investigations, especially in vivo.

Evidence for a frontoparietal control system revealed by intrinsic functional connectivity

Two functionally distinct, and potentially competing, brain networks have been recently identified that can be broadly distinguished by their contrasting roles in attention to the external world versus internally directed mentation involving long-term memory. At the core of these two networks are the dorsal attention system and the hippocampal-cortical memory system, a component of the brain's default network. Here spontaneous blood-oxygenation-level-dependent (BOLD) signal correlations were used in three separate functional magnetic resonance imaging data sets (n = 105) to define a third system, the frontoparietal control system, which is spatially interposed between these two previously defined systems. The frontoparietal control system includes many regions identified as supporting cognitive control and decision-making processes including lateral prefrontal cortex, anterior cingulate cortex, and inferior parietal lobule. Detailed analysis of frontal and parietal cortex, including use of high-resolution data, revealed clear evidence for contiguous but distinct regions: in general, the regions associated with the frontoparietal control system are situated between components of the dorsal attention and hippocampal-cortical memory systems. The frontoparietal control system is therefore anatomically positioned to integrate information from these two opposing brain systems.

A population-average MRI-based atlas collection of the rhesus macaque

Magnetic resonance imaging (MRI) studies of non-human primates are becoming increasingly common; however, the well-developed voxel-based methodologies used in human studies are not readily applied to non-human primates. In the present study, we create a population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to creating a publicly available T1-weighted atlas (http://www.brainmap.wisc.edu/monkey.html), probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem, K.S. and Logothetis, N.K. (2006) atlas providing an explicit link to histological sections. Additionally, we have created a transform to integrate these atlases with the F99 surface-based atlas in CARET. It is anticipated that these tools will help facilitate voxel-based imaging methodologies in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.

A method for localizing microelectrode trajectories in the macaque brain using MRI

Magnetic resonance imaging (MRI) is often used by electrophysiologists to target specific brain regions for placement of microelectrodes. However, the effectiveness of this technique has been limited by few methods to quantify in three dimensions the relative locations of brain structures, recording chambers and microelectrode trajectories. Here we present such a method. After surgical implantation, recording chambers are fitted with a plastic cylinder that is filled with a high-contrast agent to aid in the segmentation of the cylinder from brain matter in an MRI volume. The resulting images of the filled cylinder correspond to a virtual cylinder that is projected along its long axis - parallel to the trajectories of microelectrodes advanced through the recording chamber - through the three-dimensional image of the brain. This technique, which does not require a stereotaxic coordinate system, can be used to quantify the coverage of an implanted recording chamber relative to anatomical landmarks at any depth or orientation. We have used this technique in conjunction with Caret [Van Essen DC, Drury HA, Dickson J, Harwell J, Hanlon D, Anderson CH. An integrated software suite for surface-based analyses of cerebral cortex. J Am Med Inform Assoc 2001;8:443-59] and AFNI [Cox RW. AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput Biomed Res 1996;29:162-73] brain-mapping software to successfully localize several regions of macaque cortex, including the middle temporal area, the lateral intraparietal area and the frontal eye field, and one subcortical structure, the locus coeruleus, for electrophysiological recordings.

The brain's default network: anatomy, function, and relevance to disease

Thirty years of brain imaging research has converged to define the brain's default network-a novel and only recently appreciated brain system that participates in internal modes of cognition. Here we synthesize past observations to provide strong evidence that the default network is a specific, anatomically defined brain system preferentially active when individuals are not focused on the external environment. Analysis of connectional anatomy in the monkey supports the presence of an interconnected brain system. Providing insight into function, the default network is active when individuals are engaged in internally focused tasks including autobiographical memory retrieval, envisioning the future, and conceiving the perspectives of others. Probing the functional anatomy of the network in detail reveals that it is best understood as multiple interacting subsystems. The medial temporal lobe subsystem provides information from prior experiences in the form of memories and associations that are the building blocks of mental simulation. The medial prefrontal subsystem facilitates the flexible use of this information during the construction of self-relevant mental simulations. These two subsystems converge on important nodes of integration including the posterior cingulate cortex. The implications of these functional and anatomical observations are discussed in relation to possible adaptive roles of the default network for using past experiences to plan for the future, navigate social interactions, and maximize the utility of moments when we are not otherwise engaged by the external world. We conclude by discussing the relevance of the default network for understanding mental disorders including autism, schizophrenia, and Alzheimer's disease.

The Brain Connectivity Workshops: moving the frontiers of computational systems neuroscience

Understanding the link between neurobiology and cognition requires that neuroscience moves beyond mere structure-function correlations. An explicit systems perspective is needed in which putative mechanisms of how brain function is constrained by brain structure are mathematically formalized and made accessible for experimental investigation. Such a systems approach critically rests on a better understanding of brain connectivity in its various forms. Since 2002, frontier topics of connectivity and neural system analysis have been discussed in a multidisciplinary annual meeting, the Brain Connectivity Workshop (BCW), bringing together experimentalists and theorists from various fields. This article summarizes some of the main discussions at the two most recent workshops, 2006 at Sendai, Japan, and 2007 at Barcelona, Spain: (i) investigation of cortical micro- and macrocircuits, (ii) models of neural dynamics at multiple scales, (iii) analysis of "resting state" networks, and (iv) linking anatomical to functional connectivity. Finally, we outline some central challenges and research trajectories in computational systems neuroscience for the next years.

Distinct cortical anatomy linked to subregions of the medial temporal lobe revealed by intrinsic functional connectivity

The hippocampus and adjacent cortical structures in the medial temporal lobe (MTL) contribute to memory through interactions with distributed brain areas. Studies of monkey and rodent anatomy suggest that parallel pathways converge on distinct subregions of the MTL. To explore the cortical areas linked to subregions of the MTL in humans, we examined cortico-cortical and hippocampal-cortical correlations using high-resolution, functional connectivity analysis in 100 individuals. MTL seed regions extended along the anterior to posterior axis and included hippocampus and adjacent structures. Results revealed two separate brain pathways that correlated with distinct subregions within the MTL. The body of the hippocampus and posterior parahippocampal cortex correlated with lateral parietal cortex, regions along the posterior midline including posterior cingulate and retrosplenial cortex, and ventral medial prefrontal cortex. By contrast, anterior hippocampus and the perirhinal/entorhinal cortices correlated with distinct regions in the lateral temporal cortex extending into the temporal pole. The present results are largely consistent with known connectivity in the monkey and provide a novel task-independent dissociation of the parallel pathways supporting the MTL memory system in humans. The cortical pathways include regions that have undergone considerable areal expansion in humans, providing insight into how the MTL memory system has evolved to support a diverse array of cognitive domains.

Comparing surface-based and volume-based analyses of functional neuroimaging data in patients with schizophrenia

A major challenge in functional neuroimaging is to cope with individual variability in cortical structure and function. Most analyses of cortical function compensate for variability using affine or low-dimensional nonlinear volume-based registration (VBR) of individual subjects to an atlas, which does not explicitly take into account the geometry of cortical convolutions. A promising alternative is to use surface-based registration (SBR), which capitalizes on explicit surface representations of cortical folding patterns in individual subjects. In this study, we directly compare results from SBR and affine VBR in a study of working memory in healthy controls and patients with schizophrenia (SCZ). Each subject's structural scan was used for cortical surface reconstruction using the SureFit method. fMRI data were mapped directly onto individual cortical surface models, and each hemisphere was registered to the population-average PALS-B12 atlas using landmark-constrained SBR. The precision with which cortical sulci were aligned was much greater for SBR than VBR. SBR produced superior alignment precision across the entire cortex, and this benefit was greater in patients with schizophrenia. We demonstrate that spatial smoothing on the surface provides better resolution and signal preservation than a comparable degree of smoothing in the volume domain. Lastly, the statistical power of functional activation in the working memory task was greater for SBR than for VBR. These results indicate that SBR provides significant advantages over affine VBR when analyzing cortical fMRI activations. Furthermore, these improvements can be even greater in disorders that have associated structural abnormalities.

A dual-networks architecture of top-down control

Complex systems ensure resilience through multiple controllers acting at rapid and slower timescales. The need for efficient information flow through complex systems encourages small-world network structures. On the basis of these principles, a group of regions associated with top-down control was examined. Functional magnetic resonance imaging showed that each region had a specific combination of control signals; resting-state functional connectivity grouped the regions into distinct 'fronto-parietal' and 'cingulo-opercular' components. The fronto-parietal component seems to initiate and adjust control; the cingulo-opercular component provides stable 'set-maintenance' over entire task epochs. Graph analysis showed dense local connections within components and weaker 'long-range' connections between components, suggesting a small-world architecture. The control systems of the brain seem to embody the principles of complex systems, encouraging resilient performance.