Cortical surface parcellation based on intra-subject white matter fiber clustering
CEA（法国原子能和替代能源委员会）
Narciso López-López, Andrea Vázquez, Cyril Poupon, Jean-François Mangin, Pamela Guevara
备注：
This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 690941, CONICYT PFCHA/ DOCTORADO NACIONAL/2016-21160342, CONICYT FONDECYT 1190701, CONICYT PIA/Anillo de Investigación en Ciencia y Tecnología ACT172121 and CONICYT Basal Center FB0008
We present a hybrid method that performs the complete parcellation of the cerebral cortex of an individual, based on the connectivity information of the white matter fibers from a whole-brain tractography dataset. The method consists of five steps, first intra-subject clustering is performed on the brain tractography. The fibers that make up each cluster are then intersected with the cortical mesh and then filtered to discard outliers. In addition, the method resolves the overlapping between the different intersection regions (sub-parcels) throughout the cortex efficiently. Finally, a post-processing is done to achieve more uniform sub-parcels. The output is the complete labeling of cortical mesh vertices, representing the different cortex sub-parcels, with strong connections to other sub-parcels. We evaluated our method with measures of brain connectivity such as functional segregation (clustering coefficient), functional integration (characteristic path length) and small-world. Results in five subjects from ARCHI database show a good individual cortical parcellation for each one, composed of about 200 subparcels per hemisphere and complying with these connectivity measures.
JParc: Joint cortical surface parcellation with registration
1 Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, MGH \& HMS 2 Center for Neurotechnology；Neurorecovery, Department of Neurology, MGH \& HMS 3 Computer Science；Artificial Intelligence Laboratory, EECS, MIT
We present cortical surface parcellation using spherical deep convolutional neural networks. Traditional multi-atlas cortical surface parcellation requires inter-subject surface registration using geometric features with high processing time on a single subject (2-3 hours). Moreover, even optimal surface registration does not necessarily produce optimal cortical parcellation as parcel boundaries are not fully matched to the geometric features. In this context, a choice of training features is important for accurate cortical parcellation. To utilize the networks efficiently, we propose cortical…
Ludwig-Maximilians-University（慕尼黑大学）；Technical University of Munich（慕尼黑工业大学）
The reconstruction of cerebral cortex surfaces from brain MRI scans is instrumental for the analysis of brain morphology and the detection of cortical thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover, for a fine-grained analysis of atrophy patterns, the parcellation of the cortical surfaces into individual brain regions is required. For the former task, powerful deep learning approaches, which provide highly accurate brain surfaces of tissue boundaries from input MRI scans in seconds, have recently been proposed. However, these methods do not come with the ability…
Imperial College of Science, Technology and Medicine（帝国理工学院（科学、技术与医学））；Imperial College London（伦敦帝国学院）
In this thesis, we present robust and fully-automated methods for the subdivision of the entire human cerebral cortex based on connectivity information. Our contributions are four-fold: First, we propose a clustering approach to delineate a cortical parcellation that provides a reliable abstraction of the brain's functional organisation. Second, we cast the parcellation problem as a feature reduction problem and make use of manifold learning and image segmentation techniques to identify cortical regions with distinct structural connectivity patterns. Third, we present a multi-layer graphical m…
One of the primary objectives of human brain mapping is the division of the cortical surface into functionally distinct regions, i.e. parcellation. While it is generally agreed that at macro-scale different regions of the cortex have different functions, the exact number and configuration of these regions is not known. Methods for the discovery of these regions are thus important, particularly as the volume of available information grows. Towards this end, we present a parcellation method based on a Bayesian non-parametric mixture model of cortical connectivity.
The parcellation of the primate cerebral cortex into numbered regions, based on cytoarchitecture, began with the pioneering research of neuroanatomist Kobrinian Brodmann. While the borders between regions have changed somewhat, and in some cases continue to be disputed, the idea of dividing the cortex into distinct numbered areas has become central to the goal of understanding brain function. And indeed, areal maps do provide a good starting point for functional parcellation. It is obvious, for example, that visual area V1 has a different function than primary motor cortex. However, as with an…
Current theories hold that brain function is highly related to long-range physical connections through axonal bundles, namely extrinsic connectiv-ity. However, obtaining a groupwise cortical parcellation based on extrinsic connectivity remains challenging. Current parcellation methods are compu-tationally expensive; need tuning of several parameters or rely on ad-hoc constraints. Furthermore, none of these methods present a model for the cortical extrinsic connectivity of the cortex. To tackle these problems, we propose a parsimonious model for the extrinsic connectivity and an efficient parce…
We study the distribution of brain and cortical area sizes [parcellation units (PUs)] obtained for three species: mouse, macaque, and human. We find that the distribution of PU sizes is close to lognormal. We analyze the mathematical model of evolution of brain parcellation based on iterative fragmentation and specialization. In this model, each existing PU has a probability to be split that depends on PU size only. This model shows that the same evolutionary process may have led to brain parcellation in these three species. Our model suggests that region-to-region (macro) connectivity is give…
We present a continuous model for structural brain connectivity based on the Poisson point process. The model treats each streamline curve in a tractography as an observed event in connectome space, here a product space of cortical white matter boundaries. We approximate the model parameter via kernel density estimation. To deal with the heavy computational burden, we develop a fast parameter estimation method by pre-computing associated Legendre products of the data, leveraging properties of the spherical heat kernel. We show how our approach can be used to assess the quality of cortical parc…
Large-scale functional networks have been extensively studied using resting state functional magnetic resonance imaging. However, the pattern, organization, and function of fine-scale network activity remain largely unknown. Here we characterized the spontaneously emerging visual cortical activity by applying independent component analysis to resting state fMRI signals exclusively within the visual cortex. In this sub-system scale, we observed about 50 spatially independent components that were reproducible within and across subjects, and analyzed their spatial patterns and temporal relationsh…
A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School（哈佛医学院麻省总医院A.A.马丁诺斯生物医学成像中心）；Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室）
Non-rigid cortical registration is an important and challenging task due to the geometric complexity of the human cortex and the high degree of inter-subject variability. A conventional solution is to use a spherical representation of surface properties and perform registration by aligning cortical folding patterns in that space. This strategy produces accurate spatial alignment but often requires a high computational cost. Recently, convolutional neural networks (CNNs) have demonstrated the potential to dramatically speed up volumetric registration. However, due to distortions introduced by p…
German Center for Neurodegenerative Diseases (DZNE)（德国神经退行性疾病中心（DZNE））；A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital（麻省总医院A.A.马丁诺斯生物医学成像中心）；Harvard Medical School（哈佛医学院）；MIT（麻省理工学院）
Traditional neuroimage analysis pipelines involve computationally intensive, time-consuming optimization steps, and thus, do not scale well to large cohort studies with thousands or tens of thousands of individuals. In this work we propose a fast and accurate deep learning based neuroimaging pipeline for the automated processing of structural human brain MRI scans, replicating FreeSurfer's anatomical segmentation including surface reconstruction and cortical parcellation. To this end, we introduce an advanced deep learning architecture capable of whole brain segmentation into 95 classes. The n…
CytoNet: A Foundation Model for the Human Cerebral Cortex at Cellular Resolution
Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich（神经科学与医学研究所（INM-1），贾格尔研究中心）；Helmholtz AI, Research Centre Jülich（海德堡人工智能，贾格尔研究中心）；Institute for Brain Research, University Hospital Düsseldorf（脑研究所在杜塞尔多夫大学医院）；Institute of Computational Biology, Computational Health Center, Helmholtz Munich（计算生物学研究所，计算健康中心，海德堡慕尼黑）；Institute for Stroke and Dementia Research (ISD), LMU University Hospital, LMU Munich（中风与痴呆研究所以（ISD），慕尼黑大学医院，慕尼黑大学）；Computer Vision, Institute for Computational Visualistics, University of Koblenz（计算机视觉，计算视觉研究所，科布伦兹大学）
JOSA: Joint surface-based registration and atlas construction of brain geometry and function
McGovern Institute for Brain Research, MIT（麦戈文脑科学研究所（麻省理工学院））；Harvard University（哈佛大学）；Computer Science and Artificial Intelligence Laboratory, MIT（计算机科学与人工智能实验室（麻省理工学院））
In this paper, we present an EEG study of two music improvisation experiments. Professional musicians with high level of improvisation skills were asked to perform music either according to notes (composed music) or in improvisation. Each piece of music was performed in two different modes: strict mode and "let-go" mode. Synchronized EEG data was measured from both musicians and listeners. We used one of the most reliable causality measures: conditional mutual information from mixed embedding (MIME), to analyze directed correlations between different EEG channels, which was combined with netwo…
Spike synchrony, which occurs in various cortical areas in response to specific perception, action and memory tasks, has sparked a long-standing debate on the nature of temporal organization in cortex. One prominent view is that this type of synchrony facilitates the binding or grouping of separate stimulus components. We argue instead for a more general function: A measure of the prior probability of incoming stimuli, implemented by long-range, horizontal, intra-cortical connections. We show that networks of this kind -- pulse-coupled excitatory spiking networks in a noisy environment -- can …
Hybrid Spiking Neural Networks for Low-Power Intra-Cortical Brain-Machine Interfaces
Karlsruhe Institute of Technology, Karlsruhe, Germany（卡尔斯鲁厄理工大学）；FZI Research Center for Information Technology, Karlsruhe, Germany（弗劳恩霍夫信息与通信技术研究中心）；Infineon Technologies, Dresden, Germany（英飞凌科技）
We present a model of a coupled system of the olfactory bulb and cortex. Odor inputs to the epithelium are transformed to oscillatory bulbar activities. The cortex recognizes the odor by resonating to the bulbar oscillating pattern when the amplitude and phase patterns from the bulb match an odor memory stored in the intracortical synapses. We assume a cortical structure which transforms the odor information in the oscillatory pattern to a slow DC feedback signal to the bulb. This feedback suppresses the bulbar response to the pre-existing odor, allowing subsequent odor objects to be segmented…
Neural correlations during a cognitive task are central to study brain information processing and computation. However, they have been poorly analyzed due to the difficulty of recording simultaneous single neurons during task performance. In the present work, we quantified neural directional correlations using spike trains that were simultaneously recorded in sensory, premotor, and motor cortical areas of two monkeys during a somatosensory discrimination task. Upon modeling spike trains as binary time series, we used a nonparametric Bayesian method to estimate pairwise directional correlations…
Neurons in primary auditory cortex (AI) in the ferret (Mustela putorius) that are well described by their spectro-temporal response field (STRF), are found also to have a distinctive property that we call temporal symmetry. For temporally symmetric neurons, every temporal cross-section of the STRF (impulse response) is given by the same function of time, except for a scaling and a "Hilbert rotation". This property held in 85% of neurons (123 out of 145) recorded from awake animals, and in 96% of neurons (70 out of 73) recorded from anesthetized animals. This property of temporal symmetry is hi…
Randomly-connected networks of integrate-and-fire (IF) neurons are known to display asynchronous irregular (AI) activity states, which resemble the discharge activity recorded in the cerebral cortex of awake animals. However, it is not clear whether such activity states are specific to simple IF models, or if they also exist in networks where neurons are endowed with complex intrinsic properties similar to electrophysiological measurements. Here, we investigate the occurrence of AI states in networks of nonlinear IF neurons, such as the adaptive exponential IF (Brette-Gerstner-Izhikevich) mode…
Power spectra of awake resting state EEG recordings in humans typically have an Alpha peak at around 10 Hz riding a decreasing background "Xi process". Normal and pathological variations may have more than one peak or none. The single channel Xi-Alpha model (Pascual-Marqui et al 1988, https://doi.org/10.3109/00207458808985730) separated these two processes, providing a low-dimensional parametric description of EEG spectra. Currently lacking is a generative whole cortex model for activity spectra and intracortical functional connectivity. Here we introduce the "cortical Xi-Alpha model". The cro…
While many human imaging methodologies probe the structural and functional connectivity of the brain, techniques to investigate cortical networks in a causal and directional manner are critical but limited. The use of iEEG enables several approaches to directly characterize brain regions that are functionally connected and in some cases also establish directionality of these connections. In this chapter we focus on the basis, method and application of the cortico-cortical evoked potential (CCEP), whereby electrical pulses applied to one set of intracranial electrodes yields an electrically-ind…
Analyzing the brain in terms of organizational structures at intermediate scales provides an approach to negotiate the complexity arising from interactions between its large number of components. Focusing on a wiring diagram that spans the cortex, basal ganglia and thalamus of the Macaque brain, we provide a mesoscopic-level description of the topological architecture of one of the most well-studied mammalian connectomes. The robust modules we identify each comprise densely inter-connected cortical and sub-cortical areas that play complementary roles in executing specific cognitive functions. …
Thermodynamic criticality describes emergent phenomena in a wide variety of complex systems. In the mammalian brain, the complex dynamics that spontaneously emerge from neuronal interactions have been characterized as neuronal avalanches, a form of critical branching dynamics. Here, we show that neuronal avalanches also reflect that the brain dynamics are organized close to a thermodynamic critical point. We recorded spontaneous cortical activity in monkeys and humans at rest using high-density intracranial microelectrode arrays and magnetoencephalography, respectively. By numerically changing…
Detailed delineation of the fetal brain in diffusion MRI via multi-task learning
Harvard Medical School（哈佛医学院）；Elmhurst Hospital Center（埃尔姆赫斯特医院中心）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；Massachusetts General Hospital（麻省总医院）；University of California Irvine（加州大学欧文分校）
SurfAge-Net: A Hierarchical Surface-Based Network for Interpretable Fine-Grained Brain Age Prediction
Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University（甘肃省可穿戴计算重点实验室，信息科学与工程学院，兰州大学）；Department of Medical Imaging Center, Gansu Provincial Maternity and Child-Care Hospital（医学影像中心，甘肃省妇幼保健院）；Department of Magnetic Resonance, Lanzhou University Second Hospital（磁共振科，兰州大学第二医院）；Department of Computer Science and Technology, Harbin Institute of Technology (Shenzhen)（计算机科学与技术系，哈尔滨工业大学（深圳））；Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University（教育部生物医学工程重点实验室，生物医学工程学院，浙江大学）
We measured the impact of long-range exponentially decaying intra-areal lateral connectivity on the scaling and memory occupation of a distributed spiking neural network simulator compared to that of short-range Gaussian decays. While previous studies adopted short-range connectivity, recent experimental neurosciences studies are pointing out the role of longer-range intra-areal connectivity with implications on neural simulation platforms. Two-dimensional grids of cortical columns composed by up to 11 M point-like spiking neurons with spike frequency adaption were connected by up to 30 G syna…
During mechanical ventilation, patient-ventilator disharmony is frequently observed and may result in increased breathing effort, compromising the patient's comfort and recovery. This circumstance requires clinical intervention and becomes challenging when verbal communication is difficult. In this work, we propose a brain computer interface (BCI) to automatically and non-invasively detect patient-ventilator disharmony from electroencephalographic (EEG) signals: a brain-ventilator interface (BVI). Our framework exploits the cortical activation provoked by the inspiratory compensation when the …
