Three-dimensional atlases of subcortical brain structures are valuable tools to reference anatomy in neuroscience and neurology. For instance, they can be used to study the position and shape of the ...three most common deep brain stimulation (DBS) targets, the subthalamic nucleus (STN), internal part of the pallidum (GPi) and ventral intermediate nucleus of the thalamus (VIM) in spatial relationship to DBS electrodes. Here, we present a composite atlas based on manual segmentations of a multimodal high resolution brain template, histology and structural connectivity. In a first step, four key structures were defined on the template itself using a combination of multispectral image analysis and manual segmentation. Second, these structures were used as anchor points to coregister a detailed histological atlas into standard space. Results show that this approach significantly improved coregistration accuracy over previously published methods. Finally, a sub-segmentation of STN and GPi into functional zones was achieved based on structural connectivity. The result is a composite atlas that defines key nuclei on the template itself, fills the gaps between them using histology and further subdivides them using structural connectivity. We show that the atlas can be used to segment DBS targets in single subjects, yielding more accurate results compared to priorly published atlases. The atlas will be made publicly available and constitutes a resource to study DBS electrode localizations in combination with modern neuroimaging methods.
•Composite subcortical atlas based on a multimodal, high definition MNI template series, histology and tractography.•High definition atlas of DBS targets matching MNI 152 NLIN 2009b space.•Tractography based parcellation of the two primary DBS target regions STN and GPi into functional zones.•Multimodal subcortical segmentation algorithm applied to MNI template.
Brain stimulation, a therapy increasingly used for neurological and psychiatric disease, traditionally is divided into invasive approaches, such as deep brain stimulation (DBS), and noninvasive ...approaches, such as transcranial magnetic stimulation. The relationship between these approaches is unknown, therapeutic mechanisms remain unclear, and the ideal stimulation site for a given technique is often ambiguous, limiting optimization of the stimulation and its application in further disorders. In this article, we identify diseases treated with both types of stimulation, list the stimulation sites thought to be most effective in each disease, and test the hypothesis that these sites are different nodes within the same brain network as defined by resting-state functional-connectivity MRI. Sites where DBS was effective were functionally connected to sites where noninvasive brain stimulation was effective across diseases including depression, Parkinson's disease, obsessive-compulsive disorder, essential tremor, addiction, pain, minimally conscious states, and Alzheimer's disease. A lack of functional connectivity identified sites where stimulation was ineffective, and the sign of the correlation related to whether excitatory or inhibitory noninvasive stimulation was found clinically effective. These results suggest that resting-state functional connectivity may be useful for translating therapy between stimulation modalities, optimizing treatment, and identifying new stimulation targets. More broadly, this work supports a network perspective toward understanding and treating neuropsychiatric disease, highlighting the therapeutic potential of targeted brain network modulation.
The human cerebellum is involved in language, motor tasks and cognitive processes such as attention or emotional processing. Therefore, an automatic and accurate segmentation method is highly ...desirable to measure and understand the cerebellum role in normal and pathological brain development. In this work, we propose a patch-based multi-atlas segmentation tool called CERES (CEREbellum Segmentation) that is able to automatically parcellate the cerebellum lobules. The proposed method works with standard resolution magnetic resonance T1-weighted images and uses the Optimized PatchMatch algorithm to speed up the patch matching process. The proposed method was compared with related recent state-of-the-art methods showing competitive results in both accuracy (average DICE of 0.7729) and execution time (around 5 minutes).
Display omitted
•We present a novel method for cerebellum lobule segmentation on MRI.•The method consists of a fast multi-atlas non-local patch-based label fusion.•Our proposed method was shown to improve the state-of-the-art methods with a reduced temporal cost (5 minutes).•The pipeline presented in this work will be made available to scientific community through our web -based platform volBrain.
The volumetric quantification of brain structures is of great interest in pediatric populations because it allows the investigation of different factors influencing neurodevelopment. FreeSurfer and ...FSL both provide frequently used packages for automatic segmentation of brain structures. In this study, we examined the accuracy and consistency of those two automated protocols relative to manual segmentation, commonly considered as the “gold standard” technique, for estimating hippocampus and amygdala volumes in a sample of preadolescent children aged between 6 to 11years. The volumes obtained with FreeSurfer and FSL-FIRST were evaluated and compared with manual segmentations with respect to volume difference, spatial agreement and between- and within-method correlations.
Results highlighted a tendency for both automated techniques to overestimate hippocampus and amygdala volumes, in comparison to manual segmentation. This was more pronounced when using FreeSurfer than FSL-FIRST and, for both techniques, the overestimation was more marked for the amygdala than the hippocampus. Pearson correlations support moderate associations between manual tracing and FreeSurfer for hippocampus (right r=0.69, p<0.001; left r=0.77, p<0.001) and amygdala (right r=0.61, p<0.001; left r=0.67, p<0.001) volumes. Correlation coefficients between manual segmentation and FSL-FIRST were statistically significant (right hippocampus r=0.59, p<0.001; left hippocampus r=0.51, p<0.001; right amygdala r=0.35, p<0.001; left amygdala r=0.31, p<0.001) but were significantly weaker, for all investigated structures. When computing intraclass correlation coefficients between manual tracing and automatic segmentation, all comparisons, except for left hippocampus volume estimated with FreeSurfer, failed to reach 0.70. When looking at each method separately, correlations between left and right hemispheric volumes showed strong associations between bilateral hippocampus and bilateral amygdala volumes when assessed using manual segmentation or FreeSurfer. These correlations were significantly weaker when volumes were assessed with FSL-FIRST. Finally, Bland–Altman plots suggest that the difference between manual and automatic segmentation might be influenced by the volume of the structure, because smaller volumes were associated with larger volume differences between techniques.
These results demonstrate that, at least in a pediatric population, the agreement between amygdala and hippocampus volumes obtained with automated FSL-FIRST and FreeSurfer protocols and those obtained with manual segmentation is not strong. Visual inspection by an informed individual and, if necessary, manual correction of automated segmentation outputs are important to ensure validity of volumetric results and interpretation of related findings.
•In a pediatric sample, we compare hippocampus and amygdala volumes from FSL-FIRST and FreeSurfer to manual segmentation•We examine discrepancies, associations, and biases between automatic and manual segmentation volumes•In the studied pediatric population, the agreement between manual segmentation, FreeSurfer and FSL is questionable•Associations between manual segmentation and FreeSurfer were stronger than with FSL-FIRST•Associations between manual segmentation and automatic techniques were stronger for hippocampus than amygdala volumes
Brain size variation over primate evolution and human development is associated with shifts in the proportions of different brain regions. Individual brain size can vary almost twofold among ...typically developing humans, but the consequences of this for brain organization remain poorly understood. Using in vivo neuroimaging data from more than 3000 individuals, we find that larger human brains show greater areal expansion in distributed frontoparietal cortical networks and related subcortical regions than in limbic, sensory, and motor systems. This areal redistribution recapitulates cortical remodeling across evolution, manifests by early childhood in humans, and is linked to multiple markers of heightened metabolic cost and neuronal connectivity. Thus, human brain shape is systematically coupled to naturally occurring variations in brain size through a scaling map that integrates spatiotemporally diverse aspects of neurobiology.
Though commonly thought of as a “motor structure”, we now know that the cerebellum's reciprocal connections to the cerebral cortex underlie contributions to both motor and non-motor behavior. ...Further, recent research has shown that cerebellar dysfunction may contribute to a wide range of neuropsychiatric disorders. However, there has been little characterization of normative variability at the level of cerebellar structure that can facilitate and further our understanding of disease biomarkers. In this manuscript we examine normative variation of the cerebellum using data from the Human Connectome Project (HCP). The Multiple Automatically Generated Templates (MAGeT) segmentation tool was used to identify the cerebella and 33 anatomically-defined lobules from 327 individuals from the HCP. To characterize normative variation, we estimated population mean volume and variability, assessed differences in hemisphere and sex, and related lobular volume to motor and non-motor behavior. We found that the effects of hemisphere and sex were not homogeneous across all lobules of the cerebellum. Greater volume in the right hemisphere was primarily driven by lobules Crus I, II, and H VIIB, with H VIIIA exhibiting the greatest left>right asymmetry. Relative to total cerebellar gray-matter volume, females had larger Crus II (known to be connected with non-motor regions of the cerebral cortex) while males had larger motor-connected lobules including H V, and VIIIA/B. When relating lobular volume to memory, motor performance, and emotional behavior, we found some evidence for relationships that have previously been identified in the literature. Our observations of normative cerebellar structure and variability in young adults provide evidence for lobule-specific differences in volume and the relationship with sex and behavior – indicating that the cerebellum cannot be considered a single structure with uniform function, but as a set of regions with functions that are likely as diverse as their connectivity with the cerebral cortex.
•Examination of normative cerebellar structure in a healthy sample of young adults.•Provides an estimation of raw and relative lobular volumes.•Identification of differential lobule-specific sex and hemispheric differences.•Support for larger cerebella in males, with differential lobule-specific sex differences.•Identification of nominal relationships with cognitive and performance variables.
The cerebellum's involvement in cognitive, affective and motor functions is mediated by connections to different regions of the cerebral cortex. A distinctive feature of cortico-cerebellar loops that ...has been demonstrated in the animal work is a topographic organization that is preserved across its corticopontine, pontocerebellar, and cerebello-thalmo-cortical segments. Here we used tractography derived from diffusion imaging data to characterize the connections between the pons and the individual lobules of the cerebellum and generate a parcellation of the pons and middle cerebellar peduncle based on the pattern of connectivity. We identified a rostral to caudal gradient in the pons, similar to that observed in the animal work, such that rostral regions were preferentially connected to cerebellar lobules involved in non-motor, and caudal regions with motor regions. These findings advance our fundamental understanding of the cerebellum, and the parcellations we generated provide context for future research into the pontocerebellar tract's involvement in health and disease.
It was recently proposed that olfaction evolved to aid navigation. Consistent with this hypothesis, olfactory identification and spatial memory are linked to overlapping brain areas which include the ...orbitofrontal cortex and hippocampus. However, the relationship between these two processes has never been specifically investigated. Here, we show that olfactory identification covaries with spatial memory in humans. We also found that the cortical thickness of the left medial orbitofrontal cortex, and the volume of the right hippocampus, predict both olfactory identification and spatial memory. Finally, we demonstrate deficits in both olfactory identification and spatial memory in patients with lesions of the medial orbitofrontal cortex. Our findings reveal an intrinsic relationship between olfaction and spatial memory that is supported by a shared reliance on the hippocampus and medial orbitofrontal cortex. This relationship may find its roots in the parallel evolution of the olfactory and hippocampal systems.
As humans age, a characteristic pattern of widespread neocortical dendritic disruption coupled with compensatory effects in hippocampus and other subcortical structures is shown in postmortem ...investigations. It is now possible to address age-related effects on gray matter (GM) neuritic organization and density in humans using multishell diffusion-weighted MRI and the neurite-orientation dispersion and density imaging (NODDI) model. In 45 healthy individuals across the adult lifespan (21-84 years), we used a multishell diffusion imaging and the NODDI model to assess the intraneurite volume fraction and neurite orientation-dispersion index (ODI) in GM tissues. We also determined the functional correlates of variations in GM microstructure by obtaining resting-state fMRI and behavioral data. We found a significant age-related deficit in neocortical ODI (most prominently in frontoparietal regions), whereas increased ODI was observed in hippocampus and cerebellum with advancing age. Neocortical ODI outperformed cortical thickness and white matter fractional anisotropy for the prediction of chronological age in the same individuals. Higher GM ODI sampled from resting-state networks with known age-related susceptibility (default mode and visual association networks) was associated with increased functional connectivity of these networks, whereas the task-positive networks tended to show no association or even decreased connectivity. Frontal pole ODI mediated the negative relationship of age with executive function, whereas hippocampal ODI mediated the positive relationship of age with executive function. Our in vivo findings align very closely with the postmortem data and provide evidence for vulnerability and compensatory neural mechanisms of aging in GM microstructure that have functional and cognitive impact in vivo.
PDF
