Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
Individual functional atlasing of the human brain with multitask fMRI data: l...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
This document summarizes a meeting that discussed analyzing naturalistic fMRI data using the Fast Shared Response Model (FastSRM). It described the Individual Brain Charting dataset, analyzing clips and raiders tasks with FastSRM, evaluating reproducibility through cross-validation, and finding consistent retinotopic maps and semantic space across subjects. The document concluded that FastSRM is a computationally efficient method for analyzing naturalistic fMRI data.
Individual functional atlasing of the human brain with multitask fMRI data: l...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
Functional specialization in human cognition: a large-scale neuroimaging init...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault [1]. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. To date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) dataset stands for a high-resolution multi-task fMRI dataset that intends to provide a framework toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort (12 participants) performing many different tasks, free from both inter-subject and inter-site variability. The first release of the IBC dataset is already out and publicly available in the OpenNeuro (ds000244) and NeuroVault (id=4438). These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain, as the main findings of the original studies were reproduced at a high resolution. They thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. Additionally, this dataset supports the investigation of mega-analytic encoding models to be implemented in a brain-atlasing infrastructure, by systematically mapping functional signatures associated with the cognitive components of the tasks.
An introduction to the Courtois NeuroMod project - intensive brain scanning of six participants (fMRI, MEG) to help train artificial neural networks. Focus on the first data release cneuromod-2020
This document summarizes a presentation on using convolutional deep belief networks (CDBNs) for unsupervised feature learning from audio data. It describes CDBNs and how they are composed of convolutional restricted Boltzmann machines trained in a greedy layer-wise fashion. It then discusses how CDBNs were applied to unlabeled speech and music audio clips to learn hierarchical representations, which were then evaluated on speech recognition and music classification tasks. The results showed the CDBN-learned features outperformed raw audio features and MFCC features.
Individual functional atlasing of the human brain with multitask fMRI data: l...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
This document summarizes a meeting that discussed analyzing naturalistic fMRI data using the Fast Shared Response Model (FastSRM). It described the Individual Brain Charting dataset, analyzing clips and raiders tasks with FastSRM, evaluating reproducibility through cross-validation, and finding consistent retinotopic maps and semantic space across subjects. The document concluded that FastSRM is a computationally efficient method for analyzing naturalistic fMRI data.
Individual functional atlasing of the human brain with multitask fMRI data: l...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
Functional specialization in human cognition: a large-scale neuroimaging init...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault [1]. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. To date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) dataset stands for a high-resolution multi-task fMRI dataset that intends to provide a framework toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort (12 participants) performing many different tasks, free from both inter-subject and inter-site variability. The first release of the IBC dataset is already out and publicly available in the OpenNeuro (ds000244) and NeuroVault (id=4438). These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain, as the main findings of the original studies were reproduced at a high resolution. They thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. Additionally, this dataset supports the investigation of mega-analytic encoding models to be implemented in a brain-atlasing infrastructure, by systematically mapping functional signatures associated with the cognitive components of the tasks.
An introduction to the Courtois NeuroMod project - intensive brain scanning of six participants (fMRI, MEG) to help train artificial neural networks. Focus on the first data release cneuromod-2020
This document summarizes a presentation on using convolutional deep belief networks (CDBNs) for unsupervised feature learning from audio data. It describes CDBNs and how they are composed of convolutional restricted Boltzmann machines trained in a greedy layer-wise fashion. It then discusses how CDBNs were applied to unlabeled speech and music audio clips to learn hierarchical representations, which were then evaluated on speech recognition and music classification tasks. The results showed the CDBN-learned features outperformed raw audio features and MFCC features.
Individual functional atlasing of the human brain with multitask fMRI data: l...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
Deep behavioral phenotyping in functional MRI for cognitive mapping of the hu...Ana Luísa Pinho
The document summarizes a seminar given by Ana Luisa Pinho on her work analyzing the Individual Brain Charting (IBC) dataset. The IBC dataset consists of high-resolution fMRI scans of 12 healthy adults performing a variety of cognitive tasks. Pinho discussed assessing the quality of data in the IBC First Release, functional mapping of individual brains using the dataset, and encoding analysis of natural stimuli using the Fast Shared Response Model on the IBC Third Release. The goal is to leverage the large, high-quality IBC dataset to better map the relationship between brain systems and mental functions.
Deep behavioral phenotyping in functional MRI for cognitive mapping of the hu...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required, by pooling data or results from different single-task studies. Meta-analyses allow the accumulation of knowledge across studies. Yet, they are typically impacted not only by inter-subject and inter-site variability but also loss of information from sparse peak-coordinate representations. In this talk, I will address a battery of studies, which combine deep phenotyping and multitask-fMRI approaches to extensively investigate the functional signatures of the different components that characterize the human behavior. First, I will describe a set of experiments, based on temporally controlled task designs, reported in [1], [2] and [3], in which we leverage a collection of source task-fMRI data from the Individual Brain Charting (IBC) dataset. The main goal herein is to investigate the feasibility of performing individual functional brain atlasing, free from inter-subject and inter-site variability, as an effort to establish an univocal relationship between functional segregation of brain regions and elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. In addition, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network. Second, I will describe our ongoing work on the quality-assessment and validation of a subset of tasks from IBC dataset based on naturalistic stimuli using a Fast Shared Response Model encoding experiment [4]. I will finish this presentation with some insights about the application of the aforementioned functional-atlasing techniques to probe region-specific topographies linked to a particular neurocognitive mechanism of interest.
[1] Pinho, A.L. et al. (2021) DOI: 10.1002/hbm.25189
[2] Pinho, A.L. et al. (2018) DOI: 10.1038/sdata.2018.105
[3] Pinho, A.L. et al. (2020) DOI: 10.1038/s41597-020-00670-4
[4] Richard, H. et al. (2019) DOI: 10.48550/arXiv.1909.12537
An overview on EEG-based brain-computer interfaces with some fun examples from the entertainment industry. Also introducing the open-source brain-computer interface OpenBCI.
This document summarizes an article that appeared in a journal published by Elsevier. The article examines differences in brain activation patterns between schizophrenia patients and healthy controls during a simple target detection task using fMRI. The key findings were that schizophrenia patients failed to deactivate default mode network regions like the posterior cingulate cortex during the task, and they activated the dorsal attention network rather than the executive network that healthy controls activated. These results support theories of dysfunctional recruitment of large-scale brain networks in schizophrenia.
These are the slides presented by Vladimir Litvak in the Open Science Panel discussion at the BIOMAG 2018 meeting in Philadelphia. See also https://www.frontiersin.org/research-topics/5158
Fmri and neural imaging technology has advanced our understanding of how the ...Ozella Brundidge
Neuroimaging technology such as the functional magnetic resonance imaging (fMRI) and the diffusion tensor imaging (DTI) helped to reveal the phonological, semantic, and sentence clusters of the brain's language distribution networks. Technological advances in computer imaging software revealed areas where there were differences in blood oxygen level-dependent (BOLD) signal activation in response to either external and internal stimuli such as light or thinking respectively. Researchers are able to perform whole brain analysis to locate activation or deactivation, or microstructural connectivity strength, tissue alteration, or anatomical impairment.
The document presents the status report of the DPHEP collaboration, which was formed in July 2014 by seven large funding agencies to address the issue of sustainable data preservation in high energy physics (HEP). It discusses the progress made over the past 3 years, including reports from various HEP labs and experiments on their data preservation programs and initiatives. It also reviews DPHEP's common projects, the scientific potential of preserved data, and models of HEP data preservation.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
INHIBITION AND SET-SHIFTING TASKS IN CENTRAL EXECUTIVE FUNCTION OF WORKING ME...sipij
Understanding of neuro-dynamics of a complex higher cognitive process, Working Memory (WM) is
challenging. In WM, information processing occurs through four subsystems: phonological loop, visual
sketch pad, memory buffer and central executive function (CEF). CEF plays a principal role in WM. In this
study, our objective was to understand the neurospatial correlates of CEF during inhibition and set-shifting
processes. Thirty healthy educated subjects were selected. Event-Related Potential (ERP) related to visual
inhibition and set-shifting task was collected using 32 channel EEG system. Activation of those ERPs
components was analyzed using amplitudes of positive and negative peaks. Experiment was controlled
using certain parametric constraints to judge behavior, based on average responses in order to establish
relationship between ERP and local area of brain activation and represented using standardized low
resolution brain electromagnetic tomography. The average score of correct responses was higher for
inhibition task (87.5%) as compared to set-shifting task (59.5%). The peak amplitude of neuronal activity
for inhibition task was lower compared to set-shifting task in fronto-parieto-central regions. Hence this
proposed paradigm and technique can be used to measure inhibition and set-shifting neuronal processes in
understanding pathological central executive functioning in patients with neuro-psychiatric disorders.
Analyzing Complex Problem Solving by Dynamic Brain Networks.pdfNancy Ideker
This study analyzed complex problem solving using dynamic brain networks estimated from fMRI data collected while subjects played the Tower of London (TOL) game. A novel computational model was proposed that represented the brain network as an artificial neural network, with edge weights corresponding to relationships between anatomical regions. Dynamic brain networks were estimated from preprocessed fMRI signals using this neural network model. Network properties were analyzed to identify regions of interest and subgroups during planning and execution phases of TOL. Results found more hubs during planning and more strongly connected clusters, providing insights into the cognitive processes underlying complex problem solving.
This document discusses localization of language regions in the brain using electrocorticography (ECoG). It compares using a natural conversation versus a directed language task to activate language areas. The hypothesis that natural conversation could localize the same language regions as the task was not supported, as different electrode activations were found between the two methods. However, natural conversation did activate additional regions in the parietal grid. The technique requires more refinement before clinical use but may help refine electrocortical stimulation mapping.
Towards reproducibility and maximally-open dataPablo Bernabeu
Presented at the Open Scholarship Prize Competition 2021, organised by Open Scholarship Community Galway.
Video of the presentation: https://nuigalway.mediaspace.kaltura.com/media/OSW2021A+OSCG+Open+Scholarship+Prize+-+The+Final!/1_d7ekd3d3/121659351#t=56:08
Ivy Zhu, Research Scientist, Intel at MLconf SEA - 5/01/15MLconf
Model-Based Machine Learning for Real-Time Brain Decoding: Neurofeedback derived from real-time functional magnetic resonance imaging (rtfMRI) is promising for both scientific applications, such as uncovering hidden brain networks that respond to stimulus, and clinical applications, such as helping people cope with brain disorders ranging from addiction to autism. One of the greatest challenges in applying machine learning to real time brain “decoding” is that traditional methods fit per-voxel parameters, leading to large computational problems on relatively small datasets. As such, it is easy to over-fit parameters to noise rather than the desired signals. Bayesian model-based hierarchical topographical factor analysis (HTFA) solves this problem by uncovering low-dimensional representations (latent factors) of brain images, fitting parameters for latent factors (rather than voxels) while removing the false assumption that all voxels are independent. In this talk, we’ll discuss the promise of using this and other model-based machine learning to better understand full-brain activity and functional connectivity. And we’ll show how Intel Labs and its partners are combining neuroscience and computer science expertise to further extend such algorithms for real-time brain decoding.
- Researchers used a hierarchical convolutional neural network (CNN) optimized for object categorization performance to predict neural responses in higher visual cortex.
- The top layer of the CNN accurately predicted responses in inferior temporal (IT) cortex, and intermediate layers predicted responses in V4 cortex.
- This suggests that biological performance optimization directly shaped neural mechanisms in visual processing areas, as the CNN was not explicitly trained on neural data but emerged as predictive of responses in IT and V4.
The document discusses issues with computational scientific software and proposes a solution called Digital Scientific Notations. Current scientific software is difficult to test and validate due to a lack of specifications and documentation. This makes the software results unverifiable and prevents comparison of different models. The proposed Digital Scientific Notations would embed computational models and methods into scholarly documents using a formal programming language. This would allow models to be precisely defined, validated, and compared, addressing current verification and reproducibility problems in computational science.
Deep behavioral phenotyping in functional MRI for cognitive mapping of the hu...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required, by pooling data or results from different single-task studies. Meta-analyses allow the accumulation of knowledge across studies. Yet, they are typically impacted not only by inter-subject and inter-site variability but also loss of information from sparse peak-coordinate representations. In this talk, I will address a battery of studies, which combine deep phenotyping and multitask-fMRI approaches to extensively investigate the functional signatures of the different components that characterize the human behavior. First, I will describe a set of experiments, based on temporally controlled task designs, reported in [1], [2] and [3], in which we leverage a collection of source task-fMRI data from the Individual Brain Charting (IBC) dataset. The main goal herein is to investigate the feasibility of performing individual functional brain atlasing, free from inter-subject and inter-site variability, as an effort to establish an univocal relationship between functional segregation of brain regions and elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. In addition, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network. Second, I will describe our ongoing work on the quality-assessment and validation of a subset of tasks from the IBC dataset based on naturalistic stimuli using two types of encoding models: the unsupervised Fast Shared Response Model [4], and a feature-defined model based on Deep Convolutional Neural Networks [5, 6].
[1] Pinho, A.L. et al. (2021) DOI: 10.1002/hbm.25189
[2] Pinho, A.L. et al. (2018) DOI: 10.1038/sdata.2018.105
[3] Pinho, A.L. et al. (2020) DOI: 10.1038/s41597-020-00670-4
[4] Richard, H. et al. (2019) DOI: 10.48550/arXiv.1909.12537
[5] Eickenberg, M. et al. (2016) DOI: 10.1016/j.neuroimage.2016.10.001
[6] Güçlü, U. and van Gerven, M. A. J. (2015) DOI: 10.1523/JNEUROSCI.5023-14.2015
Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Cornell Medical School, Physiology, Biophysics and Systems Biology (PBSB) graduate program, 2009.01.26, 16:00-17:00; [I:CORNELL-PBSB] (Long networks talk, incl. the following topics: why networks w. amsci*, funnygene*, net. prediction intro, memint*, tse*, essen*, sandy*, metagenomics*, netpossel*, tyna*+ topnet*, & pubnet* . Fits easily into 60’ w. 10’ questions. PPT works on mac & PC and has many photos w. EXIF tag kwcornellpbsb .)
Date Given: 01/26/2009
How to design stimulus presentation for a task-fMRI experimentAna Luísa Pinho
The document discusses how to design stimulus presentation for a task-fMRI experiment. It explains that the goal is to induce psychological states in the subject and detect related brain signals. There are two main types of experimental designs: blocked designs, where similar events are grouped, and event-related designs, where events are mixed. Key psychological considerations for stimulus design include maintaining stimulus predictability, maximizing time on task, and avoiding unintended psychological activity. The level of predictability influences a subject's psychological state, and short stimuli are recommended to keep subjects engaged in the intended task.
How to conduct and fMRI experiment in cognitive neuroscienceAna Luísa Pinho
This document outlines the steps to conduct an fMRI experiment in cognitive neuroscience. It discusses prescreening participants and obtaining consent during recruitment. It describes the MRI scanner setup, including the control room and placing participants inside the scanner. The key steps of an experiment are running a localizer scan, anatomical scan, setting the field of view, and running the functional EPI sequence. Resources provided include Western's ethics guidelines and a textbook on fMRI.
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Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. The Individual Brain Charting (IBC) project stands for a high-resolution (1.5mm), multi-task fMRI dataset, intended to provide an objective basis for the establishment of a neurocognitive atlas based on the individual mapping of the human brain. This data collection refers to a permanent cohort during performance of a wide variety of tasks across many sessions. Data up to the third release---comprising 28 tasks---are publicly available in the OpenNeuro repository (ds002685). Derived statistical maps from the first and second releases can be found in NeuroVault (id6618) and they amount for 205 canonical contrasts described on the basis of 113 cognitive concepts taken from the Cognitive Atlas. These derivatives reveal all together a comprehensive brain coverage of regions engaged in cognitive processes as well as a successful encoding of the functional networks reported by the original studies. As the dataset becomes larger and the ensuing collection of concepts gets richer, finer subject-specific, cognitive topographies can be extracted from the data. We thus explore this individual-functional-atlasing approach in order to link functional segregation of specialized brain regions to elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. Lastly, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network.
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Deep behavioral phenotyping in functional MRI for cognitive mapping of the hu...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required, by pooling data or results from different single-task studies. Meta-analyses allow the accumulation of knowledge across studies. Yet, they are typically impacted not only by inter-subject and inter-site variability but also loss of information from sparse peak-coordinate representations. In this talk, I will address a battery of studies, which combine deep phenotyping and multitask-fMRI approaches to extensively investigate the functional signatures of the different components that characterize the human behavior. First, I will describe a set of experiments, based on temporally controlled task designs, reported in [1], [2] and [3], in which we leverage a collection of source task-fMRI data from the Individual Brain Charting (IBC) dataset. The main goal herein is to investigate the feasibility of performing individual functional brain atlasing, free from inter-subject and inter-site variability, as an effort to establish an univocal relationship between functional segregation of brain regions and elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. In addition, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network. Second, I will describe our ongoing work on the quality-assessment and validation of a subset of tasks from IBC dataset based on naturalistic stimuli using a Fast Shared Response Model encoding experiment [4]. I will finish this presentation with some insights about the application of the aforementioned functional-atlasing techniques to probe region-specific topographies linked to a particular neurocognitive mechanism of interest.
[1] Pinho, A.L. et al. (2021) DOI: 10.1002/hbm.25189
[2] Pinho, A.L. et al. (2018) DOI: 10.1038/sdata.2018.105
[3] Pinho, A.L. et al. (2020) DOI: 10.1038/s41597-020-00670-4
[4] Richard, H. et al. (2019) DOI: 10.48550/arXiv.1909.12537
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The document discusses issues with computational scientific software and proposes a solution called Digital Scientific Notations. Current scientific software is difficult to test and validate due to a lack of specifications and documentation. This makes the software results unverifiable and prevents comparison of different models. The proposed Digital Scientific Notations would embed computational models and methods into scholarly documents using a formal programming language. This would allow models to be precisely defined, validated, and compared, addressing current verification and reproducibility problems in computational science.
Deep behavioral phenotyping in functional MRI for cognitive mapping of the hu...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required, by pooling data or results from different single-task studies. Meta-analyses allow the accumulation of knowledge across studies. Yet, they are typically impacted not only by inter-subject and inter-site variability but also loss of information from sparse peak-coordinate representations. In this talk, I will address a battery of studies, which combine deep phenotyping and multitask-fMRI approaches to extensively investigate the functional signatures of the different components that characterize the human behavior. First, I will describe a set of experiments, based on temporally controlled task designs, reported in [1], [2] and [3], in which we leverage a collection of source task-fMRI data from the Individual Brain Charting (IBC) dataset. The main goal herein is to investigate the feasibility of performing individual functional brain atlasing, free from inter-subject and inter-site variability, as an effort to establish an univocal relationship between functional segregation of brain regions and elementary mental functions. Results show that individual topographies---common to all tasks---are consistently mapped within and, to a lesser extent, across participants. Besides, prediction scores associated with the reconstruction of contrasts of one task from the remaining ones reveal the quantitative contribution of each task to these common representations. Yet, scores decreased when subjects were permuted between train and test, confirming that topographies are driven by subject-specific variability. In addition, we demonstrate how cognitive mapping can benefit from contrasts accumulation, by analyzing the functional fingerprints of a set of individualized regions-of-interest from the language network. Second, I will describe our ongoing work on the quality-assessment and validation of a subset of tasks from the IBC dataset based on naturalistic stimuli using two types of encoding models: the unsupervised Fast Shared Response Model [4], and a feature-defined model based on Deep Convolutional Neural Networks [5, 6].
[1] Pinho, A.L. et al. (2021) DOI: 10.1002/hbm.25189
[2] Pinho, A.L. et al. (2018) DOI: 10.1038/sdata.2018.105
[3] Pinho, A.L. et al. (2020) DOI: 10.1038/s41597-020-00670-4
[4] Richard, H. et al. (2019) DOI: 10.48550/arXiv.1909.12537
[5] Eickenberg, M. et al. (2016) DOI: 10.1016/j.neuroimage.2016.10.001
[6] Güçlü, U. and van Gerven, M. A. J. (2015) DOI: 10.1523/JNEUROSCI.5023-14.2015
Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Cornell Medical School, Physiology, Biophysics and Systems Biology (PBSB) graduate program, 2009.01.26, 16:00-17:00; [I:CORNELL-PBSB] (Long networks talk, incl. the following topics: why networks w. amsci*, funnygene*, net. prediction intro, memint*, tse*, essen*, sandy*, metagenomics*, netpossel*, tyna*+ topnet*, & pubnet* . Fits easily into 60’ w. 10’ questions. PPT works on mac & PC and has many photos w. EXIF tag kwcornellpbsb .)
Date Given: 01/26/2009
Similar to Individual functional atlasing of the human brain with multitask fMRI data: leveraging the IBC dataset (20)
How to design stimulus presentation for a task-fMRI experimentAna Luísa Pinho
The document discusses how to design stimulus presentation for a task-fMRI experiment. It explains that the goal is to induce psychological states in the subject and detect related brain signals. There are two main types of experimental designs: blocked designs, where similar events are grouped, and event-related designs, where events are mixed. Key psychological considerations for stimulus design include maintaining stimulus predictability, maximizing time on task, and avoiding unintended psychological activity. The level of predictability influences a subject's psychological state, and short stimuli are recommended to keep subjects engaged in the intended task.
How to conduct and fMRI experiment in cognitive neuroscienceAna Luísa Pinho
This document outlines the steps to conduct an fMRI experiment in cognitive neuroscience. It discusses prescreening participants and obtaining consent during recruitment. It describes the MRI scanner setup, including the control room and placing participants inside the scanner. The key steps of an experiment are running a localizer scan, anatomical scan, setting the field of view, and running the functional EPI sequence. Resources provided include Western's ethics guidelines and a textbook on fMRI.
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Music SDTB: Probing the Neurocognitive Mechanisms of Temporal PredictionsAna Luísa Pinho
This document outlines a study called the Music Single-Domain Task Battery (Music-SDTB) that aims to investigate the neurocognitive mechanisms underlying temporal predictions. The study will test 25 participants using 6 tasks that manipulate timing and sensory domains to probe the contributions of the basal ganglia and cerebellum in forming temporal predictions in rhythmic and non-rhythmic sequences. Key hypotheses are that the basal ganglia contributes more to rhythmic timing judgments while the cerebellum contributes more to single interval timing judgments. Results will provide insights into the role of different brain regions and sensory modalities in temporal prediction.
Revisiting publication at Nature Neuroscience in 2009 by Kriegeskorte, N. et al. on "Circular analysis in systems neuroscience: the dangers of double dipping"
Single-Domain Task Battery (SDTB) on Temporal PredictionAna Luísa Pinho
This document summarizes a single-domain task battery (SDTB) study on temporal prediction using fMRI. The study aims to assess whether temporal predictions are mediated by context-specific or common neurocognitive mechanisms. It outlines three models of temporal prediction and references a behavioral study that found a double dissociation between rhythmic and single-interval predictions, implicating separate roles of the cerebellum and basal ganglia. The SDTB study will use different tasks manipulating timing and sensory domains to investigate the neural correlates associated with these sub-cortical contributions and their relationship to cortex. Participants will complete production and perception tasks with auditory and visual stimuli in beat and interval conditions.
Segregation of functional territories in individual brainsAna Luísa Pinho
Aims
FMRI allows for characterization of brain activations in response to behavior. However, cognitive neuroscience is limited to group-level effects on specific tasks. Pooling data from different task-fMRI studies free from inter-subject and inter-site variability is mandatory toward a fine functional profile of cognitive atoms. We present the Individual Brain Charting dataset --concerning fMRI data acquired at high resolution (1.5mm) in the same environment and cohort-- and investigate the feasibility of individual functional atlasing using a rich taskwise dataset.
Methods
Individual z-maps from the 60 main contrasts across tasks were estimated to capture significant functional signatures. These derivatives were analyzed as in Pinho et al. (2018). Besides, contrasts were decomposed using dictionary-learning into individual networks featuring neural correlates common to the tasks. To gain insights about these commonalities, we also reconstructed contrasts from the remaining ones in a cross-validation experiment. Additionally, we delineated the cognitive profile of 6 regions-of-interest and assessed whether voxels were correctly assigned to these regions across participants.
Results
Individual components were consistently mapped and tasks were well predicted from one another. Yet, scores decreased when subjects were permuted between train and test, showing that topographies are driven by subject-specific anatomo-functional characteristics. Additionally, characterization of regions-of-interest from many contrasts objectively establishes functional specialization, supported by prediction accuracies of voxel classification.
Conclusions
Successful predictions revealed the existence of a latent structure underlying different tasks, illustrating the benefit of system-level, multi-task brain mapping. Contrasts and, subsequently, individual topographies are increasing with the latest releases, allowing for better brain-atlasing frameworks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault [1]. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
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Linking brain systems and mental functions requires accurate descriptions of behavioral tasks and fine demarcations of brain regions. Functional Magnetic Resonance Imaging (fMRI) has contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a permanent cohort performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The first release of the IBC dataset consists of data acquired from thirteen participants during performance of a dozen of tasks. Raw data from this release are publicly available in the OpenNeuro repository and derived statistical maps can be found in NeuroVault. These maps reveal a successful cognitive encoding of many psychological domains in large areas of the human brain. Indeed, main findings of the original studies were replicated at higher resolution. Our results thus provide a comprehensive revision of the neural correlates underlying behavior, highlighting nonetheless the spatial variability of functional signatures between participants. In addition, this dataset supports investigations using alternative approaches to group-level analysis of task-specific studies. For instance, such rich task-wise dataset can be applied to mega-analytic encoding models towards the development of a brain-atlasing framework, by systematically mapping functional signatures associated with the cognitive components of the tasks.
Individual Brain Charting, a high-resolution fMRI dataset for cognitive mappi...Ana Luísa Pinho
Mapping functional neuroanatomy of the human brain has become a central challenge in cognitive neuroscience and it constitutes an essential step toward linking brain systems and behavior. While there is a rich literature on the neural correlates underlying performance of standardized tasks, little is still known about the overall functional organization of the brain and how it can be translated into cognition. Neuroimaging techniques, such as Functional Magnetic Resonance Imaging (fMRI) have contributed to the investigation of brain regions involved in a variety of cognitive processes. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms within a broader scope. The Individual Brain Charting (IBC) project stands for a multi-task fMRI dataset, to be shared with the neuroimaging community, featuring an univocal encoding between task descriptors and brain imaging data. It is intended to support the investigation of the functional principles underlying the cognitive representation of the human brain, allowing for (e.g.) a detailed parcellation of the brain volume into functional-specialized regions. Additionally, the IBC project pertains to the development of a neurocognitive atlas based on the functional signatures of mutual cognitive components between task descriptors.
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As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
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The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
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With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
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equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
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concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
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Individual functional atlasing of the human brain with multitask fMRI data: leveraging the IBC dataset
1. Diedrichsen Lab online seminar
@ALuisaPinho
Individual functional atlasing of the human brain with
multitask fMRI data: leveraging the IBC dataset
Ana Lu´ısa Pinho, Ph.D.
Parietal Team
Inria Saclay – ˆIle-de-France
NeuroSpin, CEA-Saclay
France
4th of January, 2021
3. Background and motivations (1/2)
In cognitive neuroscience:
Brain systems
⇐⇒
Mental functions
tackle one psychological domain
2/22
4. Background and motivations (1/2)
In cognitive neuroscience:
Brain systems
⇐⇒
Mental functions
tackle one psychological domain
be specific enough to accurately isolate brain processes
2/22
5. Background and motivations (1/2)
In cognitive neuroscience:
Brain systems
⇐⇒
Mental functions
tackle one psychological domain
be specific enough to accurately isolate brain processes
⇓
Very hard to achieve!
Lack of generality.
6. Background and motivations (1/2)
In cognitive neuroscience:
Brain systems
⇐⇒
Mental functions
Task-fMRI experiments allow to:
link brain systems to behavior
map neural activity at mm-scale
2/22
7. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings cognitive annotations
low inter-subject variability sufficient multi-task data
3/22
8. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings cognitive annotations
low inter-subject variability sufficient multi-task data
3/22
9. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings ( ) cognitive annotations
low inter-subject variability sufficient multi-task data
3/22
10. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings ( ) cognitive annotations
low inter-subject variability sufficient multi-task data
Large-scale repositories:
OpenNeuro
NeuroVault
EBRAINS
3/22
11. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings ( ) cognitive annotations
low inter-subject variability sufficient multi-task data
Large-scale repositories:
OpenNeuro
NeuroVault
EBRAINS
Individual analysis:
Fedorenko, E. et al. (2011)
Haxby, J. et al. (2011)
Hanke, M. et al. (2014)
3/22
12. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings ( )( ) cognitive annotations
low inter-subject variability sufficient multi-task data
Large-scale repositories:
OpenNeuro
NeuroVault
EBRAINS
Individual analysis:
Fedorenko, E. et al. (2011)
Haxby, J. et al. (2011)
Hanke, M. et al. (2014)
Large-scale datasets:
HCP
studyforrest
CONNECT/Archi
3/22
13. Background and motivations (2/2)
Data-pooling analysis
Meta-analysis:
pooling data derivatives
Mega-analysis:
pooling raw data
Requisites for cognitive mapping
Minimize variability of Successful interpretation of
spatial location combined results
same processing no loss of info from sparse
routines peak-coord. representation
same experimental consistency of
settings ( )( ) cognitive annotations
low inter-subject variability sufficient multi-task data
Large-scale repositories:
OpenNeuro
NeuroVault
EBRAINS
Individual analysis:
Fedorenko, E. et al. (2011)
Haxby, J. et al. (2011)
Hanke, M. et al. (2014)
Large-scale datasets:
HCP
studyforrest
CONNECT/Archi
IBC dataset: a facility that
meets the requisites all
together
3/22
16. The IBC dataset
High spatial-resolution fMRI data (1.5mm)
TR = 2s
Task-wise dataset:
Many tasks
4/22
17. The IBC dataset
High spatial-resolution fMRI data (1.5mm)
TR = 2s
Task-wise dataset:
Many tasks
Fixed cohort - 12 healthy adults
4/22
18. The IBC dataset
High spatial-resolution fMRI data (1.5mm)
TR = 2s
Task-wise dataset:
Many tasks
Fixed cohort - 12 healthy adults
Fixed environment
NeuroSpin platform, CEA-Saclay, France
Siemens 3T Magnetom Prismafit
64-channel coil
4/22
19. The IBC dataset
High spatial-resolution fMRI data (1.5mm)
TR = 2s
Task-wise dataset:
Many tasks
Fixed cohort - 12 healthy adults
Fixed environment
Inclusion of other MRI modalities
NeuroSpin platform, CEA-Saclay, France
Siemens 3T Magnetom Prismafit
64-channel coil
4/22
20. The IBC dataset
High spatial-resolution fMRI data (1.5mm)
TR = 2s
Task-wise dataset:
Many tasks
Fixed cohort - 12 healthy adults
Fixed environment
Inclusion of other MRI modalities
Not a longitudinal study!
NeuroSpin platform, CEA-Saclay, France
Siemens 3T Magnetom Prismafit
64-channel coil
4/22
21. Tasks
First release:
ARCHI battery
Pinel, P. et al. (2007)
Standard
Spatial
Social
Emotional
HCP battery
Barch, D. M. et al. (2013)
Emotion
Gambling
Motor
Language
Relational
Social
WM
RSVP Language task
Humphries, C. et al. (2006)
Second release:
Mental Time Travel battery
Gauthier, B., & van Wassenhove, V. (2016a,b)
Preference battery
Lebreton, M. et al. (2015)
ToM + Pain Matrices battery
Dodell-Feder, D. et al. (2010)
Jacoby, N. et al. (2015)
Richardson, H. et al. (2018)
Visual Short-Term Memory +
Enumeration tasks
Knops, A. et al. (2014)
Self-Reference Effect task
Genon, S. et al. (2014)
“Bang!” task
Campbell, K. L. et al. (2015)
Third release:
Clips task
Nishimoto, S. et al. (2011)
Retinotopy task
Sereno, M. et al. (1995)
“Raiders” task
Haxby, J. V. et al. (2011)
Fourth release: (Coming up soon!)
Lyon battery
Hamam´e, C. M. et al. (2012) / Ossand´on, T. et al. (2012)
Saignavongs, M. et al. (2017) / Vidal, J. R. et al. (2010)
Perrone-Bertolotti, M. et al. (2012)
Realistic Sounds task
Santoro, R. et al. (2017)
Stanford battery
Ward, G. and Allport, A. (1997)
Shallice, T. (1992) / Stroop, J. R. (1935)
Bissett, P. G. and Logan, G. D. (2011)
Eriksen, B. A. and Eriksen, C. W. (1974) 5/22
22. Tasks
First release:
ARCHI battery
Pinel, P. et al. (2007)
Standard
Spatial
Social
Emotional
HCP battery
Barch, D. M. et al. (2013)
Emotion
Gambling
Motor
Language
Relational
Social
WM
RSVP Language task
Humphries, C. et al. (2006)
Second release:
Mental Time Travel battery
Gauthier, B., & van Wassenhove, V. (2016a,b)
Preference battery
Lebreton, M. et al. (2015)
ToM + Pain Matrices battery
Dodell-Feder, D. et al. (2010)
Jacoby, N. et al. (2015)
Richardson, H. et al. (2018)
Visual Short-Term Memory +
Enumeration tasks
Knops, A. et al. (2014)
Self-Reference Effect task
Genon, S. et al. (2014)
“Bang!” task
Campbell, K. L. et al. (2015)
Third release:
Clips task
Nishimoto, S. et al. (2011)
Retinotopy task
Sereno, M. et al. (1995)
“Raiders” task
Haxby, J. V. et al. (2011)
Fourth release: (Coming up soon!)
Lyon battery
Hamam´e, C. M. et al. (2012) / Ossand´on, T. et al. (2012)
Saignavongs, M. et al. (2017) / Vidal, J. R. et al. (2010)
Perrone-Bertolotti, M. et al. (2012)
Realistic Sounds task
Santoro, R. et al. (2017)
Stanford battery
Ward, G. and Allport, A. (1997)
Shallice, T. (1992) / Stroop, J. R. (1935)
Bissett, P. G. and Logan, G. D. (2011)
Eriksen, B. A. and Eriksen, C. W. (1974)
1st rel. + 2nd rel. + Retinotopy
All contrasts: 216
Elementary contrasts: 120
Cognitive concepts: 113
5/22
29. IBC reproduces ARCHI and HCP
talevs.mentaladdition
mentalmotionvs.random
motion
punishmentvs.reward
leftfootvs.anymotion
lefthandvs.anymotion
rightfootvs.anymotion
righthandvs.anymotion
tonguevs.anymotion
faceimagevs.shapeoutline
relationalprocessingvs.visualmatching
2-backvs.0-back
bodyimagevs.anyimage
faceimagevs.anyimage
placeimagevs.anyimage
toolimagevs.anyimage
horizontalcheckerboardvs.verticalcheckerboard
mentalsubtractionvs.sentence
readsentencevs.listentosentence
readsentencevs.checkerboard
lefthandvs.righthand
saccadevs.fixation
guesswhichhandvs.handpalm
orback
objectgraspingvs.mimicorientation
mentalmotionvs.random
motion
false-beliefstoryvs.mechanisticstory
false-belieftalevs.mechanistictale
facetrustyvs.facegender
expressionintentionvs.expressiongender
tale vs. mental addition
mental motion vs. random motion
punishment vs. reward
left foot vs. any motion
left hand vs. any motion
right foot vs. any motion
right hand vs. any motion
tongue vs. any motion
face image vs. shape outline
relational processing vs. visual matching
2-back vs. 0-back
body image vs. any image
face image vs. any image
place image vs. any image
tool image vs. any image
horizontal checkerboard vs. vertical checkerboard
mental subtraction vs. sentence
read sentence vs. listen to sentence
read sentence vs. checkerboard
left hand vs. right hand
saccade vs. fixation
guess which hand vs. hand palm or back
object grasping vs. mimic orientation
mental motion vs. random motion
false-belief story vs. mechanistic story
false-belief tale vs. mechanistic tale
face trusty vs. face gender
expression intention vs. expression gender
HCP contrasts ARCHI contrasts
IBCcontrasts
1.00
0.75
0.50
0.25
0.00
0.25
0.50
0.75
1.00 ARCHI batteries:
Pinel, P. et al. (2007)
HCP batteries:
Barch, D. M. et al. (2013)
n = 13
Pinho, A.L. et al. Hum Brain Mapp(2020)
10/22
30. Activation similarity fits task similarity
n = 11
Similarity between
activation maps
of elementary contrasts
Similarity between
cognitive description
of elementary contrasts
Pinho, A.L. et al. SciData(2020) 11/22
31. Activation similarity fits task similarity
n = 11
Similarity between
activation maps
of elementary contrasts
Similarity between
cognitive description
of elementary contrasts
Pinho, A.L. et al. SciData(2020)
Spearman correlation
First Release: 0.21 (p ≤ 10−17)
Second Release: 0.21 (p ≤ 10−13)
First+Second Releases: 0.23 (p ≤ 10−72)
11/22
33. Variability of Functional Signatures
Pinho, A.L. et al. Hum Brain Mapp(2020) n = 13
Individual z-maps
13/22
34. Variability of Functional Signatures
Pinho, A.L. et al. Hum Brain Mapp(2020) n = 13
0.00 0.25 0.50
read sentence vs. listen to sentence
read sentence vs. checkerboard
left hand vs. right hand
horizontal checkerboard vs. vertical checkerboard
mental subtraction vs. sentence
saccade vs. fixation
guess which hand vs. hand palm or back
object grasping vs. mimic orientation
mental motion vs. random motion
false-belief story vs. mechanistic story
false-belief tale vs. mechanistic tale
expression intention vs. expression gender
face trusty vs. face gender
face image vs. shape outline
punishment vs. reward
0.00 0.25 0.50
tongue vs. any motion
right foot vs. any motion
left foot vs. any motion
right hand vs. any motion
left hand vs. any motion
tale vs. mental addition
relational processing vs. visual matching
mental motion vs. random motion
tool image vs. any image
place image vs. any image
face image vs. any image
body image vs. any image
2-back vs. 0-back
read pseudowords vs. consonant strings
read words vs. consonant strings
read words vs. read pseudowords
read sentence vs. read jabberwocky
read sentence vs. read words
inter-subject correlation
intra-subject correlation
Intra- and inter- subject correlation of brain maps
13/22
36. Dictionary of cognitive components
Decomposition of 51 contrasts
with dictionary learning
Individual topographies of
20 components (n = 13)
Each component gets the name
of the active condition from the
contrast with the highest value in
the functional fingerprint.
Multi-subject, sparse dictionary learning:
min(Us )s=1...n,V∈C
n
s=1
Xs
− Us
V 2
+ λ Us
1 ,
with Xs
p×c , Us
p×k and Vk×c
Functional correspondence: dictionary
of functional profiles (V) common to
all subjects
Sparsity: 1−norm penalty and
Us ≥ 0 , ∀s ∈ [n]
15/22
37. Dictionary of cognitive components
Pinho, A.L. et al. Hum Brain Mapp(2020) n = 13
Components are consistently mapped across subjects.
15/22
38. Dictionary of cognitive components
Pinho, A.L. et al. Hum Brain Mapp(2020) n = 13
Components are consistently mapped across subjects.
15/22
39. Dictionary of cognitive components
Pinho, A.L. et al. Hum Brain Mapp(2020) n = 13
0.25 0.30 0.35 0.40 0.45 0.50 0.55
Intra-subject
correlation
Inter-subject
correlation
Correlations of the dictionary components on split-half data
Variability of topographies linked to individual differences.
15/22
41. Reconstruction of functional contrasts
Leave-p-out CV (p=3 subjects)
experiment to learn the shared
representations from contrasts of
eleven tasks. (n = 13)
Predict all contrasts from the
remaining task
17/22
42. Reconstruction of functional contrasts
Leave-p-out CV (p=3 subjects)
experiment to learn the shared
representations from contrasts of
eleven tasks. (n = 13)
Predict all contrasts from the
remaining task
Train a Ridge-regression model to predict task j
on individual contrast-maps i = s:
ws,λ,j
= argminw∈Rc−1
i=s
Xi
j −Xi
−j w 2
+λ w 2
Prediction output for one contrast of task j in
subject s:
Xs
j = Xs
−j ws,λ,j
.
Cross-validated R-squared at location i:
R2
i (j) = 1 − means∈[n]
Xs
i,j − Xs
i,j
2
Xs
i,j
2
17/22
43. Reconstruction of functional contrasts
Pinho, A.L. et al. Hum Brain Mapp(2020)
n = 13
max R2
Most of the brain regions
are covered by the
predicted functional
signatures.
17/22
44. Reconstruction of functional contrasts
n = 13
Pinho, A.L. et al. Hum Brain Mapp(2020)
Ridge-Regression model
for the scrambled case:
ws,λ,j
= argminw∈Rc−1
i,k = s
Xi
j −Xk
−j w 2
+λ w 2
Cross-validated R-squared:
R2
i (j) = 1 − means∈[n]
Xs
i,j − Xs
i,j
2
Xs
i,j
2
Permutations of subjects
decrease the proportion of
well-predicted voxels in all
tasks, showing that
topographies are driven by
subject-specific variability.
17/22
46. Ex: Functional mapping of the language network
Goal: Cognitive profile of ROIs based on IBC language-related contrasts
Select ROIs / Select IBC contrasts
Individualize ROIs using dual-regression
and the left-out contrasts
R(s) = R pinv X(s) X(s)
Voxelwise z-scores average for each
ROI at every selected contrast
Pinho, A.L. et al. Hum Brain Mapp(2020)
19/22
47. Ex: Functional mapping of the language network
Linear SVC (upper triangle)
Dummy Classifier (lower triangle)
LOGOCV scheme
Prediction within pairs of ROIs
13 groups = 13 participants
Pinho, A.L. et al. Hum Brain Mapp(2020)
19/22
48. Concluding remarks
Functional atlasing using a large dataset in the task dimension
Investigation of common functional profiles between tasks
Common
functional profiles
Shared
behavioral responses
Mental
functions
20/22
49. Concluding remarks
Functional atlasing using a large dataset in the task dimension
Investigation of common functional profiles between tasks
Common
functional profiles
Shared
behavioral responses
Mental
functions
Individual brain modeling using data with higher spatial resolution
generalize across subjects
elicit variability between subjects
20/22
50. Future outcomes
Article on the IBC-dataset third-release
Fourth release out soon!
Fifth and sixth releases out this year
21/22