Functional and structural mapping of human cerebral cortex: solutions are in the surfaces

Quantitative evaluation of LDDMM, FreeSurfer, and CARET for cortical surface mapping

Cortical surface mapping has been widely used to compensate for individual variability of cortical shape and topology in anatomical and functional studies. While many surface mapping methods were proposed based on landmarks, curves, spherical or native cortical coordinates, few studies have extensively and quantitatively evaluated surface mapping methods across different methodologies. In this study we compared five cortical surface mapping algorithms, including large deformation diffeomorphic metric mapping (LDDMM) for curves (LDDMM-curve), for surfaces (LDDMM-surface), multi-manifold LDDMM (MM-LDDMM), FreeSurfer, and CARET, using 40 MRI scans and 10 simulated datasets. We computed curve variation errors and surface alignment consistency for assessing the mapping accuracy of local cortical features (e.g., gyral/sulcal curves and sulcal regions) and the curvature correlation for measuring the mapping accuracy in terms of overall cortical shape. In addition, the simulated datasets facilitated the investigation of mapping error distribution over the cortical surface when the MM-LDDMM, FreeSurfer, and CARET mapping algorithms were applied. Our results revealed that the LDDMM-curve, MM-LDDMM, and CARET approaches best aligned the local curve features with their own curves. The MM-LDDMM approach was also found to be the best in aligning the local regions and cortical folding patterns (e.g., curvature) as compared to the other mapping approaches. The simulation experiment showed that the MM-LDDMM mapping yielded less local and global deformation errors than the CARET and FreeSurfer mappings.

Surface shape analysis with an application to brain surface asymmetry in schizophrenia

Some methods for the statistical analysis of surface shapes and asymmetry are introduced. We focus on a case study where magnetic resonance images of the brain are available from groups of 30 schizophrenia patients and 38 controls, and we investigate large-scale brain surface shape differences. Key aspects of shape analysis are to remove nuisance transformations by registration and to identify which parts of one object correspond with the parts of another object. We introduce maximum likelihood and Bayesian methods for registering brain images and providing large-scale correspondences of the brain surfaces. Brain surface size-and-shape analysis is considered using random field theory, and also dimension reduction is carried out using principal and independent components analysis. Some small but significant differences are observed between the the patient and control groups. We then investigate a particular type of asymmetry called torque. Differences in asymmetry are observed between the control and patient groups, which add strength to other observations in the literature. Further investigations of the midline plane location in the 2 groups and the fitting of nonplanar curved midlines are also considered.

Spherical demons: fast diffeomorphic landmark-free surface registration

We present the Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizors for the modified Demons objective function can be efficiently approximated on the sphere using iterative smoothing. Based on one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast. The Spherical Demons algorithm can also be modified to register a given spherical image to a probabilistic atlas. We demonstrate two variants of the algorithm corresponding to warping the atlas or warping the subject. Registration of a cortical surface mesh to an atlas mesh, both with more than 160 k nodes requires less than 5 min when warping the atlas and less than 3 min when warping the subject on a Xeon 3.2 GHz single processor machine. This is comparable to the fastest nondiffeomorphic landmark-free surface registration algorithms. Furthermore, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different applications that use registration to transfer segmentation labels onto a new image 1) parcellation of in vivo cortical surfaces and 2) Brodmann area localization in ex vivo cortical surfaces.

Imaging the human medial temporal lobe with high-resolution fMRI

High-resolution functional MRI (hr-fMRI) affords unique leverage on the functional properties of human medial temporal lobe (MTL) substructures. We review initial hr-fMRI efforts to delineate (1) encoding and retrieval processes within the hippocampal circuit, (2) hippocampal subfield contributions to pattern separation and pattern completion, and (3) the representational capabilities of distinct MTL subregions. Extant data reveal functional heterogeneity within human MTL and highlight the promise of hr-fMRI for bridging human, animal, and computational approaches to understanding MTL function.

A surface-based analysis of hemispheric asymmetries and folding of cerebral cortex in term-born human infants

We have established a population average surface-based atlas of human cerebral cortex at term gestation and used it to compare infant and adult cortical shape characteristics. Accurate cortical surface reconstructions for each hemisphere of 12 healthy term gestation infants were generated from structural magnetic resonance imaging data using a novel segmentation algorithm. Each surface was inflated, flattened, mapped to a standard spherical configuration, and registered to a target atlas sphere that reflected shape characteristics of all 24 contributing hemispheres using landmark constrained surface registration. Population average maps of sulcal depth, depth variability, three-dimensional positional variability, and hemispheric depth asymmetry were generated and compared with previously established maps of adult cortex. We found that cortical structure in term infants is similar to the adult in many respects, including the pattern of individual variability and the presence of statistically significant structural asymmetries in lateral temporal cortex, including the planum temporale and superior temporal sulcus. These results indicate that several features of cortical shape are minimally influenced by the postnatal environment.

Model-driven parameterization of the cortical surface for localization and inter-subject matching

In this paper we present a generic and organized model of cortical folding, and a way to implement this model on any given cortical surface. This results in a model-driven parameterization, providing an anatomically meaningful coordinate system for cortical localization, and implicitly defining inter-subject surface matching without any deformation of surfaces. We present our cortical folding model and show how it naturally defines a parameterization of the cortex. The mapping of the model to any given cortical surface is detailed, leading to an anatomically invariant coordinate system. The process is evaluated on real data in terms of both anatomical and functional localization, and shows improved performance compared to a traditional volume-based normalization. It is fully automatic and available with the BrainVISA software platform.

Cortical thickness or grey matter volume? The importance of selecting the phenotype for imaging genetics studies

Choosing the appropriate neuroimaging phenotype is critical to successfully identify genes that influence brain structure or function. While neuroimaging methods provide numerous potential phenotypes, their role for imaging genetics studies is unclear. Here we examine the relationship between brain volume, grey matter volume, cortical thickness and surface area, from a genetic standpoint. Four hundred and eighty-six individuals from randomly ascertained extended pedigrees with high-quality T1-weighted neuroanatomic MRI images participated in the study. Surface-based and voxel-based representations of brain structure were derived, using automated methods, and these measurements were analysed using a variance-components method to identify the heritability of these traits and their genetic correlations. All neuroanatomic traits were significantly influenced by genetic factors. Cortical thickness and surface area measurements were found to be genetically and phenotypically independent. While both thickness and area influenced volume measurements of cortical grey matter, volume was more closely related to surface area than cortical thickness. This trend was observed for both the volume-based and surface-based techniques. The results suggest that surface area and cortical thickness measurements should be considered separately and preferred over gray matter volumes for imaging genetic studies.

Hippocampal volume deficits and shape deformities in young biological relatives of schizophrenia probands

Hippocampal volume decrement may be one of the changes that most closely pre-date schizophrenia onset. Studying hippocampal developmental morphology in adolescent or young adult biological relatives of schizophrenia probands has the potential to further our understanding of the neurodevelopmental etiology of schizophrenia and to discover biomarkers that may aid its early identification. We utilized an artificial neural network segmentation algorithm to automatically define and reliably measure MRI hippocampus volumes. We compared 46 young, nonpsychotic biological relatives of probands against 46 healthy controls without family history of schizophrenia and 46 schizophrenia probands (age range=13 to 28 years). We further contrasted hippocampal shape differences using spherical harmonic functions and assessed how obstetric complications (a trigger for aberrant in utero neurodevelopment) may contribute to hippocampal abnormalities. Similar to schizophrenia probands, unaffected biological relatives of probands had significantly smaller hippocampus volumes than controls; which correspond to inward displacements in shape deformities principally in the anterior hippocampal subregions. Examination of hippocampus volume-age relationships indicate that hippocampus volume normally decreases with age during late adolescence through early adulthood. In contrast, relatives of probands did not show these age-expected changes. Deviant hippocampus volume-age relationships suggest aberrant hippocampal neurodevelopment among biological relatives. Relatives with a history of obstetric complications had significantly smaller left and right hippocampi than relatives without obstetrics complications, including a dose relationship such that greater number of birth complications correlated with smaller hippocampus. Similar hippocampal volume deficits-obstetric complications relationships were observed among schizophrenia probands. Hippocampal abnormalities in schizophrenia are likely to be mediated by different neurobiological mechanisms, including factors associated with obstetric complications which occur during early neurodevelopment. Other brain maturational anomalies affecting the hippocampus in schizophrenia may manifest closer to illness onset in adolescence/early adulthood.

Estimation of cerebral surface area using vertical sectioning and magnetic resonance imaging: a stereological study

Stereological techniques using isotropic uniform random and vertical uniform random sections have been used for surface area estimation. However, there are a few studies in which the surface area of the brain is estimated using the vertical section technique in a stereological approach. The objective of the current study was to apply the vertical section technique using cycloid test probes for estimation of cerebral surface area in magnetic resonance imaging (MRI). In this study, cerebral surface areas were estimated in a total of 13 young subjects (6 males, 7 females) who were free of any neurological symptoms and signs. The means (+/-S.D.) of the surface areas were 1619.92+/-140. 97 cm (2), 1625.69+/-147. 58 cm(2) and 1674.69+/-160. 60 cm(2) for 36, 18 and 12 vertical sections, respectively. The mean coefficient of error obtained by applying cycloid test lines that use a 2. 8-cm ratio of area associated with each cycloid was estimated at <7% for the three models. No significant difference was found for each of the 36, 18 and 12 vertical sections (p>0.05). In addition, the three models correlated well with each other. From these results, it is concluded that the vertical section technique is an unbiased, efficient and reliable method and is ideally suited to in vivo examination of MRI data for estimating the surface area of the brain. Hence, we suggest that estimation of surface area using MRI and stereology may be clinically relevant for assessing cortical atrophy as well as for investigating the structure and function of cerebral hemispheres.

Comparison of landmark-based and automatic methods for cortical surface registration

Group analysis of structure or function in cerebral cortex typically involves, as a first step, the alignment of cortices. A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark-based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis.

Multi-manifold diffeomorphic metric mapping for aligning cortical hemispheric surfaces

Cortical surface-based analysis has been widely used in anatomical and functional studies because it is geometrically appropriate for the cortex. One of the main challenges in the cortical surface-based analysis is to optimize the alignment of the cortical hemispheric surfaces across individuals. In this paper, we introduce a multi-manifold large deformation diffeomorphic metric mapping (MM-LDDMM) algorithm that allows simultaneously carrying the cortical hemispheric surface and its sulcal curves from one to the other through a flow of diffeomorphisms. We present an algorithm based on recent derivation of a law of momentum conservation for the geodesics of diffeomorphic flow. Once a template is fixed, the space of initial momentum becomes an appropriate space for studying shape via geodesic flow since the flow at any point on curves and surfaces along the geodesic is completely determined by the momentum at the origin. We solve for trajectories (geodesics) of the kinetic energy by computing its variation with respect to the initial momentum and by applying a gradient descent scheme. The MM-LDDMM algorithm optimizes the initial momenta encoding the anatomical variation of each individual relative to a common coordinate system in a linear space, which provides a natural scheme for shape deformation average and template (or atlas) generation. We applied the MM-LDDMM algorithm for constructing the templates for the cortical surface and 14 sulcal curves of each hemisphere using a group of 40 subjects. The estimated template shape reflects regions which are highly variable across these subjects. Compared with existing single-manifold LDDMM algorithms, such as the LDDMM-curve mapping and the LDDMM-surface mapping, the MM-LDDMM mapping provides better results in terms of surface to surface distances in five predefined regions.

Advancing fetal brain MRI: targets for the future

Fetal MRI is becoming an increasingly powerful imaging tool for studying brain development in vivo. Until recently, the application of advanced magnetic resonance imaging techniques was limited by motion in the nonsedated fetus. Extensive research efforts currently underway are focusing on the development of dedicated magnetic resonance imaging sequences and sophisticated postprocessing techniques that are revolutionizing our ability to study the healthy and compromised fetus. The ongoing refinement of these magnetic resonance imaging techniques will undoubtedly lead to the development of cornerstone biomarkers that will provide healthcare caregivers with vital, and currently lacking, information upon which to counsel parents effectively, and base rational decisions regarding the timing and type of novel medical and surgical interventions currently on the horizon.

Automatic cortical sulcal parcellation based on surface principal direction flow field tracking

The human cerebral cortex is a highly convoluted structure composed of sulci and gyri, corresponding to the valleys and ridges of the cortical surface respectively. Automatic parcellation of the cortical surface into sulcal regions is of great importance in structural and functional mapping of the human brain. In this paper, a novel method is proposed for automatic cortical sulcal parcellation based on the geometric characteristics of cortical surface including its principal curvatures and principal directions. This method is composed of two major steps: 1) employing the hidden Markov random field model (HMRF) and the expectation maximization (EM) algorithm on the maximum principal curvatures of the cortical surface for sulcal region segmentation, and 2) using a principal direction flow field tracking method on the cortical surface for sulcal basin segmentation. The flow field is obtained by diffusing the principal direction field on the cortical surface mesh. A unique feature of this method is that the automatic sulcal parcellation process is quite robust and efficient, and is independent of any external guidance such as atlas-based warping. The method has been successfully applied to the inner cortical surfaces of twelve healthy human brain MR images. Both quantitative and qualitative evaluation results demonstrate the validity and efficiency of the proposed method.

Prefrontal organization of cognitive control according to levels of abstraction

The prefrontal cortex (PFC) plays a crucial role in cognitive control and higher mental functions by maintaining working memory representations of currently relevant information, thereby inducing a mindset that facilitates the processing of such information. Using fMRI, we examined how the human PFC implements mindsets for information at varying levels of abstraction. Subjects solved anagrams grouped into three kinds of blocks (concrete, moderately abstract, and highly abstract) according to the degree of abstraction of their solutions. Mindsets were induced by cuing subjects at the beginning of every block as to the degree of abstraction of solutions they should look for. Different levels of abstraction were matched for accuracy and reaction time, allowing us to examine the effects of varying abstraction in the absence of variations in cognitive complexity. Mindsets for concrete, moderately abstract, and highly abstract information were associated with stronger relative recruitment of ventrolateral, dorsolateral, and rostrolateral PFC regions, respectively, suggesting a functional topography whereby increasingly anterior regions are preferentially associated with representations of increasing abstraction. Rather than being a structural property of the neurons in different prefrontal subregions, this relative specialization may reflect one of the principles according to which lateral PFC adaptively codes and organizes task-relevant information.

A conceptual cortical surface atlas

Volumetric, slice-based, 3-D atlases are invaluable tools for understanding complex cortical convolutions. We present a simple scheme to convert a slice-based atlas to a conceptual surface atlas that is easier to visualize and understand. The key idea is to unfold each slice into a one-dimensional vector, and concatenate a succession of these vectors--while maintaining as much spatial contiguity as possible--into a 2-D matrix. We illustrate our methodology using a coronal slice-based atlas of the Rhesus Monkey cortex. The conceptual surface-based atlases provide a useful complement to slice-based atlases for the purposes of indexing and browsing.

Registration based cortical thickness measurement

Cortical thickness is an important biomarker for image-based studies of the brain. A diffeomorphic registration based cortical thickness (DiReCT) measure is introduced where a continuous one-to-one correspondence between the gray matter-white matter interface and the estimated gray matter-cerebrospinal fluid interface is given by a diffeomorphic mapping in the image space. Thickness is then defined in terms of a distance measure between the interfaces of this sheet like structure. This technique also provides a natural way to compute continuous estimates of thickness within buried sulci by preventing opposing gray matter banks from intersecting. In addition, the proposed method incorporates neuroanatomical constraints on thickness values as part of the mapping process. Evaluation of this method is presented on synthetic images. As an application to brain images, a longitudinal study of thickness change in frontotemporal dementia (FTD) spectrum disorder is reported.

Transcription factor Lmo4 defines the shape of functional areas in developing cortices and regulates sensorimotor control

Proper formation of the shape and size of cortical functional areas is essential for complex brain function, including sensory perception and motor control. Our previous work identified the transcription factor Lim domain only 4 (Lmo4), a regulator in calcium-dependent gene transcription, that has unique, region-specific expression in postnatal mouse cortices with high expression anteriorly and posteriorly but very low expression in between. Here we report that Lmo4 expression coincides with the timing of the development of the somatosensory barrel field. Lmo4 cortical deletion causes changes in expression patterns of cortical regional markers and results in rostro-medial shrinkage but not rostral or caudal shift of the somatosensory barrel subfield. Fine regulation of accurate shape of the barrel subfield by Lmo4, as well as Lmo4-mediated calcium-dependent gene expression, is critical for normal brain functions, as Lmo4-deficient mice display impaired sensorimotor performance. Moreover, even though Lmo4 has broad expression in the central nervous system, it plays a subtle role in the development of non-cortical regions. Our results reveal a new mechanism of cortical area formation and normal sensorimotor control that is regulated by genes with region-specific expression in the developing cortex.

The emerging discipline of Computational Functional Anatomy

Computational Functional Anatomy (CFA) is the study of functional and physiological response variables in anatomical coordinates. For this we focus on two things: (i) the construction of bijections (via diffeomorphisms) between the coordinatized manifolds of human anatomy, and (ii) the transfer (group action and parallel transport) of functional information into anatomical atlases via these bijections. We review advances in the unification of the bijective comparison of anatomical submanifolds via point-sets including points, curves and surface triangulations as well as dense imagery. We examine the transfer via these bijections of functional response variables into anatomical coordinates via group action on scalars and matrices in DTI as well as parallel transport of metric information across multiple templates which preserves the inner product.

A geometry-driven optical flow warping for spatial normalization of cortical surfaces

Spatial normalization is frequently used to map data to a standard coordinate system by removing intersubject morphological differences, thereby allowing for group analysis to be carried out. The work presented in this paper is motivated by the need for an automated cortical surface normalization technique that will automatically identify homologous cortical landmarks and map them to the same coordinates on a standard manifold. The geometry of a cortical surface is analyzed using two shape measures that distinguish the sulcal and gyral regions in a multiscale framework. A multichannel optical flow warping procedure aligns these shape measures between a reference brain and a subject brain, creating the desired normalization. The partial differential equation that carries out the warping is implemented in a Euclidean framework in order to facilitate a multiresolution strategy, thereby permitting large deformations between the two surfaces. The technique is demonstrated by aligning 33 normal cortical surfaces and showing both improved structural alignment in manually labeled sulci and improved functional alignment in positron emission tomography data mapped to the surfaces. A quantitative comparison between our proposed surface-based spatial normalization method and a leading volumetric spatial normalization method is included to show that the surface-based spatial normalization performs better in matching homologous cortical anatomies.

Analysis of area-specific expression patterns of RORbeta, ER81 and Nurr1 mRNAs in rat neocortex by double in situ hybridization and cortical box method

BACKGROUND

The mammalian neocortex is subdivided into many areas, each of which exhibits distinctive lamina architecture. To investigate such area differences in detail, we chose three genes for comparative analyses, namely, RORbeta, ER81 and Nurr1, mRNAs of which have been reported to be mainly expressed in layers 4, 5 and 6, respectively. To analyze their qualitative and quantitative coexpression profiles in the rat neocortex, we used double in situ hybridization (ISH) histochemistry and cortical box method which we previously developed to integrate the data of different staining and individuals in a standard three-dimensional space.

PRINCIPAL FINDINGS

Our new approach resulted in three main observations. First, the three genes showed unique area distribution patterns that are mostly complementary to one another. The patterns revealed by cortical box method matched well with the cytoarchitectonic areas defined by Nissl staining. Second, at single cell level, RORbeta and ER81 mRNAs were coexpressed in a subpopulation of layer 5 neurons, whereas Nurr1 and ER81 mRNAs were not colocalized. Third, principal component analysis showed that the order of hierarchical processing in the cortex correlates well with the expression profiles of these three genes. Based on this analysis, the dysgranular zone (DZ) in the somatosensory area was considered to exhibit a profile of a higher order area, which is consistent with previous proposal.

CONCLUSIONS/SIGNIFICANCE

The tight relationship between the expression of the three layer specific genes and functional areas were revealed, demonstrating the usefulness of cortical box method in the study on the cerebral cortex. In particular, it allowed us to perform statistical evaluation and pattern matching, which would become important in interpreting the ever-increasing data of gene expression in the cortex.

Region-of-interest-based analysis with application of cortical thickness variation of left planum temporale in schizophrenia and psychotic bipolar disorder

In neuroimaging studies, spatial normalization and multivariate testing are central problems in characterizing group variation of functions (e.g., cortical thickness, curvature, functional response) in an atlas coordinate system across clinical populations. We present a region-of-interest (ROI)-based analysis framework for detecting such a group variation. This framework includes two main techniques: ROI-based registration via large deformation diffeomorphic metric surface mapping and a multivariate testing using a Gaussian random field (GRF) model on the cortical surface constructed by the eigenfunctions of the Laplace-Beltramioperator. We compared our GRF statistical model with a pointwise hypothesis testing approach, whose P-value is corrected using false discovery rate or random field theory at several smoothness scales. As an illustration, we applied this framework to a clinical study of the cortical thickness of the left planum temporale (PT) in subjects with psychotic bipolar disorder, schizophrenia, and healthy comparison controls. Our results show that the anterior portion of the left PT is thinner in the psychotic bipolar and schizophrenic groups than in the healthy control group, and the posterior portion of the left PT shows the reversal finding. Moreover, there may be a greater thickness variation in the left PT in psychotic bipolar patients when compared with that in schizophrenic patients.

Human cortical areas involved in sustaining perceptual stability during smooth pursuit eye movements

Because both, eye movements and object movements induce an image motion on the retina, eye movements must be compensated to allow a coherent and stable perception of our surroundings. The inferential theory of perception postulates that retinal image motion is compared with an internal reference signal related to eye movements. This mechanism allows to distinguish between the potential sources producing retinal image motion. Referring to this theory, we investigated referential calculation during smooth pursuit eye movements (SPEM) in humans using event-related functional magnetic resonance imaging (fMRI). The blood oxygenation level dependent (BOLD) response related to SPEM in front of a stable background was measured for different parametric steps of preceding motion stimuli and therefore assumed for different states of the referential system. To achieve optimally accurate anatomy and more detectable fMRI signal changes in group analysis, we applied cortex-based statistics both to all brain volumes and to defined regions of interest. Our analysis revealed that the activity in a temporal region as well as the posterior parietal cortex (PPC) depended on the velocity of the preceding stimuli. Previous single-cell recordings in monkeys demonstrated that the visual posterior sylvian area (VPS) is relevant for perceptual stability. The activation apparent in our study thus may represent a human analogue of this area. The PPC is known as being strongly related to goal-directed eye movements. In conclusion, temporal and parietal cortical areas may be involved in referential calculation and thereby in sustaining visual perceptual stability during eye movements.

Repairing the human brain after stroke. II. Restorative therapies

Spontaneous behavioral recovery is usually limited after stroke, making stroke a leading source of disability. A number of therapies in development aim to improve patient outcomes not by acutely salvaging threatened tissue, but instead by promoting repair and restoration of function in the subacute or chronic phase after stroke. Examples include small molecules, growth factors, cell-based therapies, electromagnetic stimulation, device-based strategies, and task-oriented and repetitive training-based interventions. Stage of development across therapies varies widely, from preclinical to late-phase clinical trials. The optimal methods to prescribe such therapies require further studies, for example, to best identify appropriate patients or to guide features of dosing. Likely, anatomic, functional, and behavioral measures of brain state, as well as measures of injury, will each be useful in this regard. Considerations for clinical trials of restorative therapies are provided, emphasizing both similarities and points of divergence with acute stroke clinical trial design.

Variability of the paracingulate sulcus and morphometry of the medial frontal cortex: associations with cortical thickness, surface area, volume, and sulcal depth

The structural and functional consequences of interindividual variations in cortical morphology are poorly understood. In this study, we examined the relationship between one well-characterized variation of the medial frontal lobes, variability of the paracingulate sulcus (PCS), and grey matter volume, cortical thickness, surface area, and sulcal depth of the adjacent anterior cingulate cortex (ACC) and paracingulate cortex (PaC). Seventy-seven healthy individuals were assigned to one of four groups depending on PCS incidence in both hemispheres: left-present, right-absent; left-absent, right-present; both absent; or both present. Comparing these groups on each measure yielded four primary findings: (1) The presence of a PCS was associated with increased PaC and decreased ACC grey matter volume in the hemisphere in which it was apparent, with an almost identical pattern being observed for surface area; (2) there was a more complex relationship between PCS variability and regional thickness, such that a PCS in the left hemisphere was associated with increased left PaC and right ACC thickness, with no comparable effects being observed for the presence of a right PCS; (3) the depths of all major left hemisphere sulci in the region were strongly positively correlated, whereas no such associations were apparent in the right hemisphere; and (4) a leftward asymmetry in PaC thickness was specifically associated with better performance on a test of spatial working memory ability. These results provide evidence for a complex interhemispheric relationship between sulcal variability and cortical morphometry, and indicate that such relationships may be important for understanding individual differences in cognitive abilities.

Speech and language functions that require a functioning Broca's area

A number of previous studies have indicated that Broca's area has an important role in understanding and producing syntactically complex sentences and other language functions. If Broca's area is critical for these functions, then either infarction of Broca's area or temporary hypoperfusion within this region should cause impairment of these functions, at least while the neural tissue is dysfunctional. The opportunity to identify the language functions that depend on Broca's area in a particular individual was provided by a patient with hyperacute stroke who showed selective hypoperfusion, with minimal infarct, in Broca's area, and acutely impaired production of grammatical sentences, comprehension of semantically reversible (but not non-reversible) sentences, spelling, and motor planning of speech articulation. When blood flow was restored to Broca's area, as demonstrated by repeat perfusion weighted imaging, he showed immediate recovery of these language functions. The identification of language functions that were impaired when Broca's area was dysfunctional (due to low blood flow) and recovered when Broca's area was functional again, provides evidence for the critical role of Broca's area in these language functions, at least in this individual.

Spherical demons: fast surface registration

We present the fast Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizers for the modified demons objective function can be efficiently implemented on the sphere using convolution. Based on the one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast - registration of two cortical mesh models with more than 100k nodes takes less than 5 minutes, comparable to the fastest surface registration algorithms. Moreover, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different settings: (1) parcellation in a set of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces.

Least-square conformal brain mapping with spring energy

The human brain cortex is a highly convoluted sheet. Mapping of the cortical surface into a canonical coordinate space is an important tool for the study of the structure and function of the brain. Here, we present a technique based on least-square conformal mapping with spring energy for the mapping of the cortical surface. This method aims to reduce the metric and area distortion while maintaining the conformal map and computation efficiency. We demonstrate through numerical results that this method effectively controls metric and area distortion, and is computational efficient. This technique is particularly useful for fast visualization of the brain cortex.

The apical dendrite theory of consciousness

The neural basis of consciousness is theorized here to be the elevated activity of the apical dendrite within a thalamocortical circuit. Both the anatomical and functional properties of these two brain structures are examined within the general context of the cortical minicolumn, which is regarded as the functional unit of the cerebral cortex. Two main circuits of the minicolumn are described: the axis circuit, which sustains activity for extended durations and produces our sensory impressions, and the shell circuit, which performs input-output processing and produces identifications, categorizations, and ideas. The apical dendrite operates within the axis circuit to stabilize neural activity, which enables conscious impressions to be steady and to be sustained over long periods of time. In an attempt to understand how the conscious aspect of subjective impressions may be related to apical dendrite activity, we examine the characteristics of the electric and magnetic fields during the movement of charges along the apical dendrite. The physical correlate of consciousness is regarded here as the relatively intense electromagnetic field that is located along the inside and the outside close to the surface of the active apical dendrite.

Improving the resolution of functional brain imaging: analyzing functional data in anatomical space

The accurate mapping of functional magnetic resonance imaging (fMRI) activations to anatomical structures is critical for fMRI studies of brain organization. In the commonly used functional space analysis method, functional images are realigned to a functional reference image and processed in low-resolution functional space. The average functional activations are then projected into high-resolution anatomical space for visualization. Here, we describe a new technique, anatomical space analysis (ASA), whereby low-resolution functional images are first coregistered and resampled directly into high-resolution anatomical space with all subsequent data processing performed in high-resolution space. A major advantage of ASA is that minor scanner sampling instabilities and small head movements can increase spatial resolution by providing multiple samples of the relationship between functional and anatomical space. Both simulations and analyses of real fMRI data show that ASA improves the precision, objectivity and reproducibility of functional brain mapping.

Reduced cortical surface area in multiple sclerosis

OBJECTIVE

To assess utility of cortical surface area as a measure of disease progression in multiple sclerosis (MS).

METHODS

We measured two-dimensional flattened cortical surface area on high-resolution magnetic resonance imaging (MRI) scans obtained in 15 subjects with clinically definite MS and ten normal subjects.

RESULTS AND DISCUSSION

Single hemisphere cortical area was reduced in MS patients compared with controls (96,451 versus 71,710 mm(2)). We found no significant relationship of cortical surface area to disability or disease duration. T2 lesion load was negatively correlated with two-dimensional cortical surface area (r=-0.62).

CONCLUSION

Cortical surface area is decreased in MS and may be a useful measure of disease progression.

Direct cortical mapping via solving partial differential equations on implicit surfaces

In this paper, we propose a novel approach for cortical mapping that computes a direct map between two cortical surfaces while satisfying constraints on sulcal landmark curves. By computing the map directly, we can avoid conventional intermediate parameterizations and help simplify the cortical mapping process. The direct map in our method is formulated as the minimizer of a flexible variational energy under landmark constraints. The energy can include both a harmonic term to ensure smoothness of the map and general data terms for the matching of geometric features. Starting from a properly designed initial map, we compute the map iteratively by solving a partial differential equation (PDE) defined on the source cortical surface. For numerical implementation, a set of adaptive numerical schemes are developed to extend the technique of solving PDEs on implicit surfaces such that landmark constraints are enforced. In our experiments, we show the flexibility of the direct mapping approach by computing smooth maps following landmark constraints from two different energies. We also quantitatively compare the metric preserving property of the direct mapping method with a parametric mapping method on a group of 30 subjects. Finally, we demonstrate the direct mapping method in the brain mapping applications of atlas construction and variability analysis.

Motor reorganization in multiple sclerosis

OBJECTIVE

To assess intra-hemispheric and interhemispheric reorganization of motor activation in multiple sclerosis (MS). Motor reorganization may contribute to minimizing motor deficits after demyelination in MS.

METHODS

We used surface-based analysis to study functional organization for motor function in ten healthy controls and in 15 MS subjects.

RESULTS AND DISCUSSION

In MS subjects, activation in the right hemisphere (ipsilateral to the hand moved) was significantly increased compared with control subjects. We interpreted this increase as interhemispheric reorganization of motor activation. The increases in right hemisphere activation were the greatest in the pre-motor cortex (Brodmann area 6) and the cognitive areas. Within the left hemisphere, contralateral to the right hand, total motor activation was not increased and the centroid of activation was not displaced when MS subjects were compared with controls. However, we found that MS subjects with high MS plaque loads showed an anterior shift of the focus of motor activation with right hand movement when compared with the low MS plaque load subjects (p<0.05). Furthermore, there was more activation in pre-motor cortex (Brodmann area 6) in the high plaque load group and less activation in sensory areas (Brodmann areas 1, 2 and 3).

CONCLUSION

Functional magnetic resonance imaging (fMRI) provides evidence that both interhemispheric and intra-hemispheric motor reorganization occur in MS.

Brain functional localization: a survey of image registration techniques

Functional localization is a concept which involves the application of a sequence of geometrical and statistical image processing operations in order to define the location of brain activity or to produce functional/parametric maps with respect to the brain structure or anatomy. Considering that functional brain images do not normally convey detailed structural information and, thus, do not present an anatomically specific localization of functional activity, various image registration techniques are introduced in the literature for the purpose of mapping functional activity into an anatomical image or a brain atlas. The problems addressed by these techniques differ depending on the application and the type of analysis, i.e., single-subject versus group analysis. Functional to anatomical brain image registration is the core part of functional localization in most applications and is accompanied by intersubject and subject-to-atlas registration for group analysis studies. Cortical surface registration and automatic brain labeling are some of the other tools towards establishing a fully automatic functional localization procedure. While several previous survey papers have reviewed and classified general-purpose medical image registration techniques, this paper provides an overview of brain functional localization along with a survey and classification of the image registration techniques related to this problem.

Gender-specific left-right asymmetries in human visual cortex

The structural correlates of gender differences in visuospatial processing are essentially unknown. Our quantitative analysis of the cytoarchitecture of the human primary visual cortex [V1/Brodmann area 17 (BA17)], neighboring area V2 (BA18), and the cytoarchitectonic correlate of the motion-sensitive complex (V5/MT+/hOc5) shows that the visual areas are sexually dimorphic and that the type of dimorphism differs among the areas. Gender differences exist in the interhemispheric asymmetry of hOc5 volumes and in the right-hemispheric volumetric ratio of hOc5 to BA17, an area that projects to V5/MT+/hOc5. Asymmetry was also observed in the surface area of hOc5 but not in its cortical thickness. The differences give males potentially more space in which to process additional information, a finding consistent with superior male processing in particular visuospatial tasks, such as mental rotation. Gender differences in hOc5 exist with similar volume fractions of cell bodies, implying that, overall, the visual neural circuitry is similar in males and females.

Imaging Brain Activation Streams from Optical Flow Computation on 2-Riemannian Manifolds

We report on mathematical methods for the exploration of spatiotemporal dynamics of Magneto- and Electro-Encephalography (MEG / EEG) surface data and/or of the corresponding brain activity at the cortical level, with high temporal resolution. In this regard, we describe how the framework and numerical computation of the optical flow--a classical tool for motion analysis in computer vision--can be extended to non-flat 2-dimensional surfaces such as the scalp and the cortical mantle. We prove the concept and mathematical well-posedness of such an extension through regularizing constraints on the estimated velocity field, and discuss the quantitative evaluation of the optical flow. The method is illustrated by simulations and analysis of brain image sequences from a ball-catching paradigm.

Neural correlates of modality-specific spatial extinction

Sites of lesions responsible for visual, tactile, and/or motor extinction have not been clearly identified. We sought to determine the frequency of extinction in various modalities immediately after acute ischemic stroke, the rate of co-occurrence of extinction across modalities, and areas of infarct and/or hypoperfusion associated with each modality of extinction. A total of 148 patients with right supratentorial stroke were studied. In Study 1, 88 patients without hemiplegia, hemianesthesia, or visual field cuts were tested within 24 hours of onset for visual, tactile, and motor extinction, and underwent magnetic resonance diffusion and perfusion imaging. Associations between modality of extinction and areas of neural dysfunction (hypoperfusion/infarct) were identified. Of the 88 patients, 19 had only tactile extinction, 8 had only visual extinction, 12 had only motor extinction, 14 had extinction in two or more modalities, and 35 had no extinction. Tactile extinction was associated with neural dysfunction in the inferior parietal lobule; visual extinction was associated with dysfunction in the visual association cortex; and motor extinction was associated with neural dysfunction in the superior temporal gyrus. In Study 2, data from 60 patients who were excluded from Study 1 because of motor deficits were analyzed in the same way to determine whether frontal lesions contributed to visual or tactile extinction. Results again demonstrated that tactile extinction is associated with inferior parietal dysfunction, and visual extinction is associated with dysfunction of the visual association cortex. Potential accounts of the results, based on the "hemisphere rivalry" model of extinction and the limited attentional capacity model, are considered.

Human cerebral cortex: a system for the integration of volume- and surface-based representations

We describe an MRI-based system for topological analysis followed by measurements of topographic features for the human cerebral cortex that takes as its starting point volumetric segmentation data. This permits interoperation between volume-based and surface-based topographic analysis and extends the functionality of many existing segmentation schemes. We demonstrate the utility of these operations in individual as well as to group analysis. The methodology integrates analyses of cortical segmentation data generated by manual and semi-automated volumetric morphometry routines (such as the program cardviews) with the procedures of the FreeSurfer program to generate a cortical ribbon of the cerebrum and perform cortical topographic measurements (including thickness, surface area and curvature) in individual subjects as well as in subject populations. This system allows the computation of topographical cortical measurements for segmentation data generated from manual and semi-automated volumetric sources other than FreeSurfer. These measurements can be regionally specific and integrated with systems of cortical parcellation that subdivides the neocortex into gyral-based parcellation units (PUs). This system of topographical analysis of the cerebral cortex is consistent with current views of cortical development and neural systems organization of the human and non-human primate brain.

Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex

We develop a novel Lagrangian reference frame diffeomorphic image and landmark registration method. The algorithm uses the fixed Langrangian reference frame to define the map between coordinate systems, but also generates and stores the inverse map from the Eulerian to the Lagrangian frame. Computing both maps allows facile computation of both Eulerian and Langrangian quantities. We apply this algorithm to estimating a putative evolutionary change of coordinates between a population of chimpanzee and human cortices. Inter-species functional homologues fix the map explicitly, where they are known, while image similarities guide the alignment elsewhere. This map allows detailed study of the volumetric change between chimp and human cortex. Instead of basing the inter-species study on a single species atlas, we diffeomorphically connect the mean shape and intensity templates for each group. The human statistics then map diffeomorphically into the space of the chimpanzee cortex providing a comparison between species. The population statistics show a significant doubling of the relative prefrontal lobe size in humans, as compared to chimpanzees.

LONI visualization environment

Over the past decade, the use of informatics to solve complex neuroscientific problems has increased dramatically. Many of these research endeavors involve examining large amounts of imaging, behavioral, genetic, neurobiological, and neuropsychiatric data. Superimposing, processing, visualizing, or interpreting such a complex cohort of datasets frequently becomes a challenge. We developed a new software environment that allows investigators to integrate multimodal imaging data, hierarchical brain ontology systems, on-line genetic and phylogenic databases, and 3D virtual data reconstruction models. The Laboratory of Neuro Imaging visualization environment (LONI Viz) consists of the following components: a sectional viewer for imaging data, an interactive 3D display for surface and volume rendering of imaging data, a brain ontology viewer, and an external database query system. The synchronization of all components according to stereotaxic coordinates, region name, hierarchical ontology, and genetic labels is achieved via a comprehensive BrainMapper functionality, which directly maps between position, structure name, database, and functional connectivity information. This environment is freely available, portable, and extensible, and may prove very useful for neurobiologists, neurogenetisists, brain mappers, and for other clinical, pedagogical, and research endeavors.

Extrinsic and intrinsic systems in the posterior cortex of the human brain revealed during natural sensory stimulation

When exposing subjects to a continuous segment of an audiovisual movie, a large expanse of human cortex, especially in the posterior half of the cerebral cortex, shows stimulus-driven activity. However, embedded within this widespread activity, there are cortical regions whose activity is dissociated from the external stimulation. These regions are intercorrelated among themselves, forming a functional network, which largely overlaps with cortical areas previously shown to be deactivated by task-oriented paradigms. Moreover, the network of areas whose neuronal dynamics are associated with external inputs and the network of areas that appears to be intrinsically driven complement each other, providing coverage of most of the posterior cortex. Thus, we propose that naturalistic stimuli reveal a fundamental neuroanatomical partition of the human posterior cortex into 2 global networks: an "extrinsic" system, comprising areas associated with the processing of external inputs, and an "intrinsic" system, largely overlapping with the task-negative, default-mode network, comprising areas associated with--as yet not fully understood--intrinsically oriented functions.