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Dr. Alexander Herman
We seek a postdoc to work on an exciting federally funded project examining cognitive effort and flexibility in traumatic brain injury (TBI). This project will use a combination of transcranial alternating current stimulation and computational modeling to improve symptoms of mental fatigue after TBI. Our interdisciplinary, joint psychiatry-neurosurgery lab offers a unique opportunity to learn or improve skills in electrophysiology, non-invasive brain stimulation, neuroeconomics, and computational modeling. The ideal candidate has a background in both engineering/computer science and cognitive neuroscience or a strong willingness to learn one or the other. The position offers the opportunity to gain experience working with patients to collect data, but strong staff support exists for this already. The focus of the post-doc will be on analyzing data and writing papers. See our website at www.hermandarrowlab.com
Prof. Li Zhaoping
Postdoctoral position in Human Visual Psychophysics with fMRI/MRI, (m/f/d) (TVöD-Bund E13, 100%) The Department of Sensory and Sensorimotor Systems (PI Prof. Li Zhaoping) at the Max Planck Institute for Biological Cybernetics and at the University of Tübingen is currently looking for highly skilled and motivated individuals to work on projects aimed towards understanding visual attentional and perceptual processes using fMRI/MRI. The framework and motivation of the projects can be found at: https://www.lizhaoping.org/zhaoping/AGZL_HumanVisual.html. The projects can involve, for example, visual search tasks, stereo vision tasks, visual illusions, and will be discussed during the application process. fMRI/MRI technology can be used in combination with other methods such as eye tracking, TMS and/or EEG methodologies, and other related methods as necessary. The postdoc will be working closely with the principal investigator and other members of Zhaoping's team when needed. Responsibilities: • Conduct and participate in research projects such as lab and equipment set up, data collection, data analysis, writing reports and papers, and presenting at scientific conferences. • Participate in routine laboratory operations, such as planning and preparations for experiments, lab maintenance and lab procedures. • Coordinate with the PI and other team members for strategies and project planning. • Coordinate with the PI and other team members for project planning, and in supervision of student projects or teaching assistance for university courses in our field. Who we are: We use a multidisciplinary approach to investigate sensory and sensory-motor transforms in the brain (www.lizhaoping.org). Our approaches consist of both theoretical and experimental techniques including human psychophysics, fMRI imaging, EEG/ERP, and computational modelling. One part of our group is located in the University, in the Centre for Integrative Neurosciences (CIN), and the other part is in the Max Planck Institute (MPI) for Biological Cybernetics as the Department for Sensory and Sensorimotor Systems. You will have the opportunity to learn other skills in our multidisciplinary group and benefit from interactions with our colleagues in the university, at MPI, as well as internationally. This job opening is for the CIN or the MPI working group. The position (salary level TVöD-Bund E13, 100%) is for a duration of two years. Extension or a permanent contract after two years is possible depending on situations. We seek to raise the number of women in research and teaching and therefore urge qualified women to apply. Disabled persons will be preferred in case of equal qualification. Your application: The position is available immediately and will be open until filled. Preference will be given to applications received by March 19th, 2023. We look forward to receiving your application that includes (1) a cover letter, including a statement on roughly when you would like to start this position, (2) a motivation statement, (3) a CV, (4) names and contact details of three people for references, (5) if you have them, transcripts from your past and current education listing the courses taken and their grades, (6) if you have them, please also include copies of your degree certificates, (7) you may include a pdf file of your best publication(s), or other documents and information that you think could strengthen your application. Please use pdf files for these documents (and you may combine them into a single pdf file) and send to jobs.li@tuebingen.mpg.de, where also informal inquiries can be addressed. Please note that applications without complete information in (1)-(4) will not be considered, unless the cover letter includes an explanation and/or information about when the needed materials will be supplied. For further opportunities in our group, please visit https://www.lizhaoping.org/jobs.html
Dr. Amy Margolis
The Environment, Brain, and Behavior (EBB) Lab for Developmental Visual-Spatial and Learning Disorders is located in the Division of Child and Adolescent Psychiatry at Columbia University Medical Center in New York City. Directed by Dr. Amy Margolis, the EBB lab studies the neurobiology of Non-Verbal Learning Disorder and how exposure to neurotoxic chemicals may affect neurodevelopment and manifest as learning and social problems. The EBB Lab uses neuroimaging to identify biomarkers of exposure to neurotoxicants and aid in the development of prevention and intervention programs to improve children's health outcomes.
Nicolas Langer
The successful candidate will work on the Synapsis-foundation funded research project “Real-life activity tracking as pre-screening tool for early stages of Alzheimer disease”. The aim of the project is to investigate whether real-life activity measures, derived from wearable technology (e.g. GPS and accelerometer data), are sensitive to identify early stages of Alzheimer’s disease. Further, we aim to provide evidence that these real-life activity measures are associated with current AD biomarkers (i.e. high Amyloid level and brain atrophy). The student will be expected to disseminate study results in peer reviewed journals, and to supervise Master’s students. The candidate will work in the team of Prof. Nicolas Langer, who is also part of the Neuroscience Center Zurich (ZNZ) (https://www.neuroscience.uzh.ch/en.html), which offers a renowned international PhD programme in Neuroscience. The candidate will work closely with the Institute for Regenerative Medicine (https://www.irem.uzh.ch/en.html), Geographic Information Systems (https://www.geo.uzh.ch/en/units/gis.html), University Research Priority Programme from the University of Zurich “Dynamics of Healthy Aging” (https://www.dynage.uzh.ch/en.html), and the Department of Computer Science at the ETH Zurich (https://www.systems.ethz.ch/). For further information, please visit: https://tinyurl.com/yvyjkvv9
Prof David Brang
We are seeking a full-time post-doctoral research fellow to study computational and neuroscientific models of perception and cognition. The research fellow will be jointly supervised by Dr. David Brang (https://sites.lsa.umich.edu/brang-lab/) and Zhongming Liu (https://libi.engin.umich.edu). The goal of this collaboration is to build computational models of cognitive and perceptual processes using data combined from electrocorticography (ECoG) and fMRI. The successful applicant will also have freedom to conduct additional research based on their interests, using a variety of methods -- ECoG, fMRI, DTI, lesion mapping, and EEG. The ideal start date is from spring to fall 2021 and the position is expected to last for at least two years, with the possibility of extension for subsequent years. We are also recruiting a Post-Doc for research on multisensory interactions (particularly how vision modulates speech perception) using Cognitive Neuroscience techniques or to help with our large-scale brain tumor collaboration with Shawn Hervey-Jumper at UCSF (https://herveyjumperlab.ucsf.edu). In this latter collaboration we collect iEEG (from ~50 patients/year) and lesion mapping data (from ~150 patients/year) in patients with a brain tumor to study sensory and cognitive functions in patients. The goals of this project are to better understand the physiology of tumors, study causal mechanisms of brain functions, and generalize iEEG/ECoG findings from epilepsy patients to a second patient population.
Dr. Jennifer Luebke
We are seeking a highly motivated and detail-oriented postdoctoral fellow with a track record in research applying magnetic resonance imaging and image processing. The central goal of the binational (Boston and Barcelona) CRCNS project is to advance our understanding of the computational and neural mechanisms underlying working memory as well as age-related changes to executive function. The successful candidate will lead analyses of structural MRI (T1 TFE scans), resting-state fMRI, and diffusion spectrum imaging (DSI) brain scans with an overall focus on brain morphometry and connectivity. Data generated from the MRI scans will be correlated with behavioral, physiological, and other anatomical data across the adult life span. This work will be part of a highly interdisciplinary project (psychophysics, imaging, anatomy, electrophysiological experiments, innovative data analysis and computational modeling) and includes the possibility for extended research stays at the Center for Mathematical Research in Barcelona, Spain (Wimmer lab). The appointment as a Boston University School of Medicine postdoctoral fellow (supervised by Jennifer Luebke and Ronald J. Killiany) will be for at least 1 year with the possibility for extension based on performance.
Departement of Movement Sciences, KU Leuven
We are looking for a dynamic and motivated individual (m/f) with an excellent research record in studying the human brain and motor behavior by means of multimodal medical techniques (such as MRI, movement registration, EEG, etc.). We offer a full-time employment in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that promotes both fundamental and applied scientific research. It is highly focused on inter- and multidisciplinary research and strives for international excellence. It provides its students with an academic education that is based on high-quality scientific research. KU Leuven aims for transparent and reproducible research. You will work in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Depending on your record and qualifications, you will be appointed to or tenured in one of the grades of the senior academic staff: assistant professor, associate professor, professor or full professor. In principle, junior researchers are appointed as assistant professor on the tenure track for a period of 5 years; after this period and contingent upon a positive evaluation, they are permanently appointed (or tenured) as associate professor. KU Leuven is well set to welcome foreign professors and their family and provides practical support with regard to immigration & administration, housing, childcare, learning Dutch, partner career coaching, … Vacancy: https://www.kuleuven.be/personeel/jobsite/jobs/55675790?hl=en&lang=en
Dr. Lei Zhang
Dr. Lei Zhang is looking for 2x PhD students interested in the cognitive, computational, and neural basis of (social) learning and decision-making in health and disease. The newly opened ALP(E)N Lab (Adaptive Learning Psychology and Neuroscience Lab) addresses the fundamental question of the “adaptive brain” by studying the cognitive, computational, and neurobiological basis of (social) learning and decision-making in healthy individuals (across the lifespan), and in psychiatric disorders. The lab combines an array of approaches including neuroimaging, patient studies and computational modelling (particularly hierarchical Bayesian modelling) with behavioural paradigms inspired by learning theories. The lab is based at the Centre for Human Brain Health and Institute of Mental Health at the University of Birmingham, UK, with access to exceptional facilities including MRI, MEG, TMS, and fNIRS. Funding is available through two competitive schemes from the BBSRC and MRC that provide a stipend, fees (at UK rate) and a research allowance, amongst other benefits. International (ie, outside UK) applicants are welcome.
Prof Mark Humphries and Dr JeYoung Yung
A 4-year fully-funded PhD studentship with Prof Mark Humphries and Dr JeYoung Yung at the University Of Nottingham is available to start September 2024. The project is titled 'Optimising patient selection for Deep Brain Stimulation in Parkinson’s disease using multimodal machine learning'. The goal of this project is to test how fusing clinical data, neuroimaging, and video assessments could optimise the selection of patients. The project will be in collaboration with MachineMedicine (London), a MedTech company specialising in Parkinson’s disease, and the movement disorders clinical team at St George’s Hospital, London. The PhD student will be trained in data-science and machine learning tools, including how to extract and analyse MRI and fMRI data, in fusing data across modalities, and in developing a machine-learning pipeline for predicting patient outcomes. These predictions will be tested against the 12-month follow-up data from the St George’s trial patients. The student’s further training will include a 3-month placement at MachineMedicine, and visits to St George’s clinic.
Susan Fischer
The 'Developmental Computational Psychiatry' lab and the W3 professorship 'Computational Psychiatry' led by Tobias Hauser at the University of Tübingen (Germany) is currently hiring new postdocs. The focus of the lab is to better understand the computational and neural mechanisms underlying decision making and learning, and how these processes go awry in patients with mental illnesses. The successful candidates will have the chance to work in a highly dynamic and inspiring environment and to collaborate closely with Prof Peter Dayan and the Max Planck Institute for Biological Cybernetics.
Susan Fischer
The 'Developmental Computational Psychiatry' lab and the W3 professorship 'Computational Psychiatry' led by Tobias Hauser at the University of Tübingen is hiring new postdocs. The lab focuses on understanding the computational and neural mechanisms underlying decision making and learning, and how these processes are affected in patients with mental illnesses. Successful candidates will work in a dynamic environment and collaborate with Prof Peter Dayan and the Max-Planck Institute for Biological Cybernetics.
John P. Spencer
The School of Psychology at the University of East Anglia has two lecturer / assistant professor posts available. We welcome applications in all areas of neuroscience – come join our outstanding faculty! We have great resources here at UEA (fNIRS, EEG, MRI, TMS, virtual reality, EyeLink 1000+, Tobii eye-trackers, mobile eye-trackers), including the newly established UEA Wellcome-Wolfson Brain Imaging Centre.
Tong (Tina) Liu, Ph.D.
A postdoc position is available in the Visual Perception and Plasticity (VPP) lab, led by Dr. Tina Liu, in the Department of Neurology at Georgetown University Medical Center. The VPP lab studies neuroplasticity in both healthy and clinical populations across the lifespan, with a focus on vision. The postdoctoral researcher will play a key role in studies that integrate psychophysics/visual behavior, eye tracking, functional and structural MRI, transcranial electrical stimulation, and computational modeling.
MRI investigation of orientation-dependent changes in microstructure and function in a mouse model of mild traumatic brain injury
OpenNeuro FitLins GLM: An Accessible, Semi-Automated Pipeline for OpenNeuro Task fMRI Analysis
In this talk, I will discuss the OpenNeuro Fitlins GLM package and provide an illustration of the analytic workflow. OpenNeuro FitLins GLM is a semi-automated pipeline that reduces barriers to analyzing task-based fMRI data from OpenNeuro's 600+ task datasets. Created for psychology, psychiatry and cognitive neuroscience researchers without extensive computational expertise, this tool automates what is largely a manual process and compilation of in-house scripts for data retrieval, validation, quality control, statistical modeling and reporting that, in some cases, may require weeks of effort. The workflow abides by open-science practices, enhancing reproducibility and incorporates community feedback for model improvement. The pipeline integrates BIDS-compliant datasets and fMRIPrep preprocessed derivatives, and dynamically creates BIDS Statistical Model specifications (with Fitlins) to perform common mass univariate [GLM] analyses. To enhance and standardize reporting, it generates comprehensive reports which includes design matrices, statistical maps and COBIDAS-aligned reporting that is fully reproducible from the model specifications and derivatives. OpenNeuro Fitlins GLM has been tested on over 30 datasets spanning 50+ unique fMRI tasks (e.g., working memory, social processing, emotion regulation, decision-making, motor paradigms), reducing analysis times from weeks to hours when using high-performance computers, thereby enabling researchers to conduct robust single-study, meta- and mega-analyses of task fMRI data with significantly improved accessibility, standardized reporting and reproducibility.
Restoring Sight to the Blind: Effects of Structural and Functional Plasticity
Visual restoration after decades of blindness is now becoming possible by means of retinal and cortical prostheses, as well as emerging stem cell and gene therapeutic approaches. After restoring visual perception, however, a key question remains. Are there optimal means and methods for retraining the visual cortex to process visual inputs, and for learning or relearning to “see”? Up to this point, it has been largely assumed that if the sensory loss is visual, then the rehabilitation focus should also be primarily visual. However, the other senses play a key role in visual rehabilitation due to the plastic repurposing of visual cortex during blindness by audition and somatosensation, and also to the reintegration of restored vision with the other senses. I will present multisensory neuroimaging results, cortical thickness changes, as well as behavioral outcomes for patients with Retinitis Pigmentosa (RP), which causes blindness by destroying photoreceptors in the retina. These patients have had their vision partially restored by the implantation of a retinal prosthesis, which electrically stimulates still viable retinal ganglion cells in the eye. Our multisensory and structural neuroimaging and behavioral results suggest a new, holistic concept of visual rehabilitation that leverages rather than neglects audition, somatosensation, and other sensory modalities.
Analyzing Network-Level Brain Processing and Plasticity Using Molecular Neuroimaging
Behavior and cognition depend on the integrated action of neural structures and populations distributed throughout the brain. We recently developed a set of molecular imaging tools that enable multiregional processing and plasticity in neural networks to be studied at a brain-wide scale in rodents and nonhuman primates. Here we will describe how a novel genetically encoded activity reporter enables information flow in virally labeled neural circuitry to be monitored by fMRI. Using the reporter to perform functional imaging of synaptically defined neural populations in the rat somatosensory system, we show how activity is transformed within brain regions to yield characteristics specific to distinct output projections. We also show how this approach enables regional activity to be modeled in terms of inputs, in a paradigm that we are extending to address circuit-level origins of functional specialization in marmoset brains. In the second part of the talk, we will discuss how another genetic tool for MRI enables systematic studies of the relationship between anatomical and functional connectivity in the mouse brain. We show that variations in physical and functional connectivity can be dissociated both across individual subjects and over experience. We also use the tool to examine brain-wide relationships between plasticity and activity during an opioid treatment. This work demonstrates the possibility of studying diverse brain-wide processing phenomena using molecular neuroimaging.
Contentopic mapping and object dimensionality - a novel understanding on the organization of object knowledge
Our ability to recognize an object amongst many others is one of the most important features of the human mind. However, object recognition requires tremendous computational effort, as we need to solve a complex and recursive environment with ease and proficiency. This challenging feat is dependent on the implementation of an effective organization of knowledge in the brain. Here I put forth a novel understanding of how object knowledge is organized in the brain, by proposing that the organization of object knowledge follows key object-related dimensions, analogously to how sensory information is organized in the brain. Moreover, I will also put forth that this knowledge is topographically laid out in the cortical surface according to these object-related dimensions that code for different types of representational content – I call this contentopic mapping. I will show a combination of fMRI and behavioral data to support these hypotheses and present a principled way to explore the multidimensionality of object processing.
LLMs and Human Language Processing
This webinar convened researchers at the intersection of Artificial Intelligence and Neuroscience to investigate how large language models (LLMs) can serve as valuable “model organisms” for understanding human language processing. Presenters showcased evidence that brain recordings (fMRI, MEG, ECoG) acquired while participants read or listened to unconstrained speech can be predicted by representations extracted from state-of-the-art text- and speech-based LLMs. In particular, text-based LLMs tend to align better with higher-level language regions, capturing more semantic aspects, while speech-based LLMs excel at explaining early auditory cortical responses. However, purely low-level features can drive part of these alignments, complicating interpretations. New methods, including perturbation analyses, highlight which linguistic variables matter for each cortical area and time scale. Further, “brain tuning” of LLMs—fine-tuning on measured neural signals—can improve semantic representations and downstream language tasks. Despite open questions about interpretability and exact neural mechanisms, these results demonstrate that LLMs provide a promising framework for probing the computations underlying human language comprehension and production at multiple spatiotemporal scales.
Introducing the 'Cognitive Neuroscience & Neurotechnolog' group: From real-time fMRI to layer-fMRI & back
Probing White Matter Microstructure With Diffusion-Weighted MRI: Techniques and Applications in ADRD
Toward globally accessible neuroimaging: Building the OSI2ONE MRI Scanner in Paraguay
The Open Source Imaging Initiative has recently released a fully open source low field MRI scanner called the OSI2ONE. We are currently building this system at the Universidad Paraguayo Alemana in Asuncion, Paraguay for a neuroimaging project at a clinic in Bolivia. I will discuss the process of construction, important considerations before you build, and future work planned with this device.
Trends in NeuroAI - Brain-like topography in transformers (Topoformer)
Dr. Nicholas Blauch will present on his work "Topoformer: Brain-like topographic organization in transformer language models through spatial querying and reweighting". Dr. Blauch is a postdoctoral fellow in the Harvard Vision Lab advised by Talia Konkle and George Alvarez. Paper link: https://openreview.net/pdf?id=3pLMzgoZSA Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri | https://groups.google.com/g/medarc-fmri).
Exploring the cerebral mechanisms of acoustically-challenging speech comprehension - successes, failures and hope
Comprehending speech under acoustically challenging conditions is an everyday task that we can often execute with ease. However, accomplishing this requires the engagement of cognitive resources, such as auditory attention and working memory. The mechanisms that contribute to the robustness of speech comprehension are of substantial interest in the context of hearing mild to moderate hearing impairment, in which affected individuals typically report specific difficulties in understanding speech in background noise. Although hearing aids can help to mitigate this, they do not represent a universal solution, thus, finding alternative interventions is necessary. Given that age-related hearing loss (“presbycusis”) is inevitable, developing new approaches is all the more important in the context of aging populations. Moreover, untreated hearing loss in middle age has been identified as the most significant potentially modifiable predictor of dementia in later life. I will present research that has used a multi-methodological approach (fMRI, EEG, MEG and non-invasive brain stimulation) to try to elucidate the mechanisms that comprise the cognitive “last mile” in speech acousticallychallenging speech comprehension and to find ways to enhance them.
Exploring Lifespan Memory Development and Intervention Strategies for Memory Decline through a Unified Model-Based Assessment
Understanding and potentially reversing memory decline necessitates a comprehensive examination of memory's evolution throughout life. Traditional memory assessments, however, suffer from a lack of comparability across different age groups due to the diverse nature of the tests employed. Addressing this gap, our study introduces a novel, ACT-R model-based memory assessment designed to provide a consistent metric for evaluating memory function across a lifespan, from 5 to 85-year-olds. This approach allows for direct comparison across various tasks and materials tailored to specific age groups. Our findings reveal a pronounced U-shaped trajectory of long-term memory function, with performance at age 5 mirroring those observed in elderly individuals with impairments, highlighting critical periods of memory development and decline. Leveraging this unified assessment method, we further investigate the therapeutic potential of rs-fMRI-guided TBS targeting area 8AV in individuals with early-onset Alzheimer’s Disease—a region implicated in memory deterioration and mood disturbances in this population. This research not only advances our understanding of memory's lifespan dynamics but also opens new avenues for targeted interventions in Alzheimer’s Disease, marking a significant step forward in the quest to mitigate memory decay.
Executive functions in the brain of deaf individuals – sensory and language effects
Executive functions are cognitive processes that allow us to plan, monitor and execute our goals. Using fMRI, we investigated how early deafness influences crossmodal plasticity and the organisation of executive functions in the adult human brain. Results from a range of visual executive function tasks (working memory, task switching, planning, inhibition) show that deaf individuals specifically recruit superior temporal “auditory” regions during task switching. Neural activity in auditory regions predicts behavioural performance during task switching in deaf individuals, highlighting the functional relevance of the observed cortical reorganisation. Furthermore, language grammatical skills were correlated with the level of activation and functional connectivity of fronto-parietal networks. Together, these findings show the interplay between sensory and language experience in the organisation of executive processing in the brain.
Trends in NeuroAI - Unified Scalable Neural Decoding (POYO)
Lead author Mehdi Azabou will present on his work "POYO-1: A Unified, Scalable Framework for Neural Population Decoding" (https://poyo-brain.github.io/). Mehdi is an ML PhD student at Georgia Tech advised by Dr. Eva Dyer. Paper link: https://arxiv.org/abs/2310.16046 Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri | https://groups.google.com/g/medarc-fmri).
Human Echolocation for Localization and Navigation – Behaviour and Brain Mechanisms
Neuromodulation of striatal D1 cells shapes BOLD fluctuations in anatomically connected thalamic and cortical regions
Understanding how macroscale brain dynamics are shaped by microscale mechanisms is crucial in neuroscience. We investigate this relationship in animal models by directly manipulating cellular properties and measuring whole-brain responses using resting-state fMRI. Specifically, we explore the impact of chemogenetically neuromodulating D1 medium spiny neurons in the dorsomedial caudate putamen (CPdm) on BOLD dynamics within a striato-thalamo-cortical circuit in mice. Our findings indicate that CPdm neuromodulation alters BOLD dynamics in thalamic subregions projecting to the dorsomedial striatum, influencing both local and inter-regional connectivity in cortical areas. This study contributes to understanding structure–function relationships in shaping inter-regional communication between subcortical and cortical levels.
Trends in NeuroAI - Meta's MEG-to-image reconstruction
Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri). Title: Brain-optimized inference improves reconstructions of fMRI brain activity Abstract: The release of large datasets and developments in AI have led to dramatic improvements in decoding methods that reconstruct seen images from human brain activity. We evaluate the prospect of further improving recent decoding methods by optimizing for consistency between reconstructions and brain activity during inference. We sample seed reconstructions from a base decoding method, then iteratively refine these reconstructions using a brain-optimized encoding model that maps images to brain activity. At each iteration, we sample a small library of images from an image distribution (a diffusion model) conditioned on a seed reconstruction from the previous iteration. We select those that best approximate the measured brain activity when passed through our encoding model, and use these images for structural guidance during the generation of the small library in the next iteration. We reduce the stochasticity of the image distribution at each iteration, and stop when a criterion on the "width" of the image distribution is met. We show that when this process is applied to recent decoding methods, it outperforms the base decoding method as measured by human raters, a variety of image feature metrics, and alignment to brain activity. These results demonstrate that reconstruction quality can be significantly improved by explicitly aligning decoding distributions to brain activity distributions, even when the seed reconstruction is output from a state-of-the-art decoding algorithm. Interestingly, the rate of refinement varies systematically across visual cortex, with earlier visual areas generally converging more slowly and preferring narrower image distributions, relative to higher-level brain areas. Brain-optimized inference thus offers a succinct and novel method for improving reconstructions and exploring the diversity of representations across visual brain areas. Speaker: Reese Kneeland is a Ph.D. student at the University of Minnesota working in the Naselaris lab. Paper link: https://arxiv.org/abs/2312.07705
Trends in NeuroAI - Meta's MEG-to-image reconstruction
Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri). This will be an informal journal club presentation, we do not have an author of the paper joining us. Title: Brain decoding: toward real-time reconstruction of visual perception Abstract: In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (≈0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (≈5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that MEG signals primarily contain high-level visual features, whereas the same approach applied to 7T fMRI also recovers low-level features. Overall, these results provide an important step towards the decoding - in real time - of the visual processes continuously unfolding within the human brain. Speaker: Dr. Paul Scotti (Stability AI, MedARC) Paper link: https://arxiv.org/abs/2310.19812
Current and future trends in neuroimaging
With the advent of several different fMRI analysis tools and packages outside of the established ones (i.e., SPM, AFNI, and FSL), today's researcher may wonder what the best practices are for fMRI analysis. This talk will discuss some of the recent trends in neuroimaging, including design optimization and power analysis, standardized analysis pipelines such as fMRIPrep, and an overview of current recommendations for how to present neuroimaging results. Along the way we will discuss the balance between Type I and Type II errors with different correction mechanisms (e.g., Threshold-Free Cluster Enhancement and Equitable Thresholding and Clustering), as well as considerations for working with large open-access databases.
Inducing short to medium neuroplastic effects with Transcranial Ultrasound Stimulation
Sound waves can be used to modify brain activity safely and transiently with unprecedented precision even deep in the brain - unlike traditional brain stimulation methods. In a series of studies in humans and non-human primates, I will show that Transcranial Ultrasound Stimulation (TUS) can have medium- to long-lasting effects. Multiple read-outs allow us to conclude that TUS can perturb neuronal tissues up to 2h after intervention, including changes in local and distributed brain network configurations, behavioural changes, task-related neuronal changes and chemical changes in the sonicated focal volume. Combined with multiple neuroimaging techniques (resting state functional Magnetic Resonance Imaging [rsfMRI], Spectroscopy [MRS] and task-related fMRI changes), this talk will focus on recent human TUS studies.
Trends in NeuroAI - SwiFT: Swin 4D fMRI Transformer
Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri). Title: SwiFT: Swin 4D fMRI Transformer Abstract: Modeling spatiotemporal brain dynamics from high-dimensional data, such as functional Magnetic Resonance Imaging (fMRI), is a formidable task in neuroscience. Existing approaches for fMRI analysis utilize hand-crafted features, but the process of feature extraction risks losing essential information in fMRI scans. To address this challenge, we present SwiFT (Swin 4D fMRI Transformer), a Swin Transformer architecture that can learn brain dynamics directly from fMRI volumes in a memory and computation-efficient manner. SwiFT achieves this by implementing a 4D window multi-head self-attention mechanism and absolute positional embeddings. We evaluate SwiFT using multiple large-scale resting-state fMRI datasets, including the Human Connectome Project (HCP), Adolescent Brain Cognitive Development (ABCD), and UK Biobank (UKB) datasets, to predict sex, age, and cognitive intelligence. Our experimental outcomes reveal that SwiFT consistently outperforms recent state-of-the-art models. Furthermore, by leveraging its end-to-end learning capability, we show that contrastive loss-based self-supervised pre-training of SwiFT can enhance performance on downstream tasks. Additionally, we employ an explainable AI method to identify the brain regions associated with sex classification. To our knowledge, SwiFT is the first Swin Transformer architecture to process dimensional spatiotemporal brain functional data in an end-to-end fashion. Our work holds substantial potential in facilitating scalable learning of functional brain imaging in neuroscience research by reducing the hurdles associated with applying Transformer models to high-dimensional fMRI. Speaker: Junbeom Kwon is a research associate working in Prof. Jiook Cha’s lab at Seoul National University. Paper link: https://arxiv.org/abs/2307.05916
NII Methods (journal club): NeuroQuery, comprehensive meta-analysis of human brain mapping
We will discuss a recent paper by Taylor et al. (2023): https://www.sciencedirect.com/science/article/pii/S1053811923002896. They discuss the merits of highlighting results instead of hiding them; that is, clearly marking which voxels and clusters pass a given significance threshold, but still highlighting sub-threshold results, with opacity proportional to the strength of the effect. They use this to illustrate how there in fact may be more agreement between researchers than previously thought, using the NARPS dataset as an example. By adopting a continuous, "highlighted" approach, it becomes clear that the majority of effects are in the same location and that the effect size is in the same direction, compared to an approach that only permits rejecting or not rejecting the null hypothesis. We will also talk about the implications of this approach for creating figures, detecting artifacts, and aiding reproducibility.
BrainLM Journal Club
Connor Lane will lead a journal club on the recent BrainLM preprint, a foundation model for fMRI trained using self-supervised masked autoencoder training. Preprint: https://www.biorxiv.org/content/10.1101/2023.09.12.557460v1 Tweeprint: https://twitter.com/david_van_dijk/status/1702336882301112631?t=Q2-U92-BpJUBh9C35iUbUA&s=19
NII Methods (journal club): NeuroQuery, comprehensive meta-analysis of human brain mapping
We will discuss this paper on Neuroquery, a relatively new web-based meta-analysis tool: https://elifesciences.org/articles/53385.pdf. This is different from Neurosynth in that it generates meta-analysis maps using predictive modeling from the string of text provided at the prompt, instead of performing inferential statistics to calculate the overlap of activation from different studies. This allows the user to generate predictive maps for more nuanced cognitive processes - especially for clinical populations which may be underrepresented in the literature compared to controls - and can be useful in generating predictions about where the activity will be for one's own study, and for creating ROIs.
Algonauts 2023 winning paper journal club (fMRI encoding models)
Algonauts 2023 was a challenge to create the best model that predicts fMRI brain activity given a seen image. Huze team dominated the competition and released a preprint detailing their process. This journal club meeting will involve open discussion of the paper with Q/A with Huze. Paper: https://arxiv.org/pdf/2308.01175.pdf Related paper also from Huze that we can discuss: https://arxiv.org/pdf/2307.14021.pdf
1.8 billion regressions to predict fMRI (journal club)
Public journal club where this week Mihir will present on the 1.8 billion regressions paper (https://www.biorxiv.org/content/10.1101/2022.03.28.485868v2), where the authors use hundreds of pretrained model embeddings to best predict fMRI activity.
In vivo direct imaging of neuronal activity at high temporospatial resolution
Advanced noninvasive neuroimaging methods provide valuable information on the brain function, but they have obvious pros and cons in terms of temporal and spatial resolution. Functional magnetic resonance imaging (fMRI) using blood-oxygenation-level-dependent (BOLD) effect provides good spatial resolution in the order of millimeters, but has a poor temporal resolution in the order of seconds due to slow hemodynamic responses to neuronal activation, providing indirect information on neuronal activity. In contrast, electroencephalography (EEG) and magnetoencephalography (MEG) provide excellent temporal resolution in the millisecond range, but spatial information is limited to centimeter scales. Therefore, there has been a longstanding demand for noninvasive brain imaging methods capable of detecting neuronal activity at both high temporal and spatial resolution. In this talk, I will introduce a novel approach that enables Direct Imaging of Neuronal Activity (DIANA) using MRI that can dynamically image neuronal spiking activity in milliseconds precision, achieved by data acquisition scheme of rapid 2D line scan synchronized with periodically applied functional stimuli. DIANA was demonstrated through in vivo mouse brain imaging on a 9.4T animal scanner during electrical whisker-pad stimulation. DIANA with milliseconds temporal resolution had high correlations with neuronal spike activities, which could also be applied in capturing the sequential propagation of neuronal activity along the thalamocortical pathway of brain networks. In terms of the contrast mechanism, DIANA was almost unaffected by hemodynamic responses, but was subject to changes in membrane potential-associated tissue relaxation times such as T2 relaxation time. DIANA is expected to break new ground in brain science by providing an in-depth understanding of the hierarchical functional organization of the brain, including the spatiotemporal dynamics of neural networks.
Attending to the ups and downs of Lewy body dementia: An exploration of cognitive fluctuations
Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) share similarities in pathology and clinical presentation and come under the umbrella term of Lewy body dementias (LBD). Fluctuating cognition is a key symptom in LBD and manifests as altered levels of alertness and attention, with a marked difference between best and worst performance. Cognition and alertness can change over seconds or minutes to hours and days of obtundation. Cognitive fluctuations can have significant impacts on the quality of life of people with LBD as well as potentially contribute to the exacerbation of other transient symptoms including, for example, hallucinations and psychosis as well as making it difficult to measure cognitive effect size benefits in clinical trials of LBD. However, this significant symptom in LBD is poorly understood. In my presentation I will discuss the phenomenology of cognitive fluctuations, how we can measure it clinically and limitations of these approaches. I will then outline the work of our group and others which has been focussed on unpicking the aetiological basis of cognitive fluctuations in LBD using a variety of imaging approaches (e.g. SPECT, sMRI, fMRI and EEG). I will then briefly explore future research directions.
Representational Connectivity Analysis (RCA): a Method for Investigating Flow of Content-Specific Information in the Brain
Representational Connectivity Analysis (RCA) has gained mounting interest in the past few years. This is because, rather than conventional tracking of signal, RCA allows for the tracking of information across the brain. It can also provide insights into the content and potential transformations of the transferred information. This presentation explains several variations of the method in terms of implementation and how it can be adopted for different modalities (E/MEG and fMRI). I will also present caveats and nuances of the method which should be considered when using the RCA.
Movement planning as a window into hierarchical motor control
The ability to organise one's body for action without having to think about it is taken for granted, whether it is handwriting, typing on a smartphone or computer keyboard, tying a shoelace or playing the piano. When compromised, e.g. in stroke, neurodegenerative and developmental disorders, the individuals’ study, work and day-to-day living are impacted with high societal costs. Until recently, indirect methods such as invasive recordings in animal models, computer simulations, and behavioural markers during sequence execution have been used to study covert motor sequence planning in humans. In this talk, I will demonstrate how multivariate pattern analyses of non-invasive neurophysiological recordings (MEG/EEG), fMRI, and muscular recordings, combined with a new behavioural paradigm, can help us investigate the structure and dynamics of motor sequence control before and after movement execution. Across paradigms, participants learned to retrieve and produce sequences of finger presses from long-term memory. Our findings suggest that sequence planning involves parallel pre-ordering of serial elements of the upcoming sequence, rather than a preparation of a serial trajectory of activation states. Additionally, we observed that the human neocortex automatically reorganizes the order and timing of well-trained movement sequences retrieved from memory into lower and higher-level representations on a trial-by-trial basis. This echoes behavioural transfer across task contexts and flexibility in the final hundreds of milliseconds before movement execution. These findings strongly support a hierarchical and dynamic model of skilled sequence control across the peri-movement phase, which may have implications for clinical interventions.
The Effects of Movement Parameters on Time Perception
Mobile organisms must be capable of deciding both where and when to move in order to keep up with a changing environment; therefore, a strong sense of time is necessary, otherwise, we would fail in many of our movement goals. Despite this intrinsic link between movement and timing, only recently has research begun to investigate the interaction. Two primary effects that have been observed include: movements biasing time estimates (i.e., affecting accuracy) as well as making time estimates more precise. The goal of this presentation is to review this literature, discuss a Bayesian cue combination framework to explain these effects, and discuss the experiments I have conducted to test the framework. The experiments herein include: a motor timing task comparing the effects of movement vs non-movement with and without feedback (Exp. 1A & 1B), a transcranial magnetic stimulation (TMS) study on the role of the supplementary motor area (SMA) in transforming temporal information (Exp. 2), and a perceptual timing task investigating the effect of noisy movement on time perception with both visual and auditory modalities (Exp. 3A & 3B). Together, the results of these studies support the Bayesian cue combination framework, in that: movement improves the precision of time perception not only in perceptual timing tasks but also motor timing tasks (Exp. 1A & 1B), stimulating the SMA appears to disrupt the transformation of temporal information (Exp. 2), and when movement becomes unreliable or noisy there is no longer an improvement in precision of time perception (Exp. 3A & 3B). Although there is support for the proposed framework, more studies (i.e., fMRI, TMS, EEG, etc.) need to be conducted in order to better understand where and how this may be instantiated in the brain; however, this work provides a starting point to better understanding the intrinsic connection between time and movement
Internal representation of musical rhythm: transformation from sound to periodic beat
When listening to music, humans readily perceive and move along with a periodic beat. Critically, perception of a periodic beat is commonly elicited by rhythmic stimuli with physical features arranged in a way that is not strictly periodic. Hence, beat perception must capitalize on mechanisms that transform stimulus features into a temporally recurrent format with emphasized beat periodicity. Here, I will present a line of work that aims to clarify the nature and neural basis of this transformation. In these studies, electrophysiological activity was recorded as participants listened to rhythms known to induce perception of a consistent beat across healthy Western adults. The results show that the human brain selectively emphasizes beat representation when it is not acoustically prominent in the stimulus, and this transformation (i) can be captured non-invasively using surface EEG in adult participants, (ii) is already in place in 5- to 6-month-old infants, and (iii) cannot be fully explained by subcortical auditory nonlinearities. Moreover, as revealed by human intracerebral recordings, a prominent beat representation emerges already in the primary auditory cortex. Finally, electrophysiological recordings from the auditory cortex of a rhesus monkey show a significant enhancement of beat periodicities in this area, similar to humans. Taken together, these findings indicate an early, general auditory cortical stage of processing by which rhythmic inputs are rendered more temporally recurrent than they are in reality. Already present in non-human primates and human infants, this "periodized" default format could then be shaped by higher-level associative sensory-motor areas and guide movement in individuals with strongly coupled auditory and motor systems. Together, this highlights the multiplicity of neural processes supporting coordinated musical behaviors widely observed across human cultures.The experiments herein include: a motor timing task comparing the effects of movement vs non-movement with and without feedback (Exp. 1A & 1B), a transcranial magnetic stimulation (TMS) study on the role of the supplementary motor area (SMA) in transforming temporal information (Exp. 2), and a perceptual timing task investigating the effect of noisy movement on time perception with both visual and auditory modalities (Exp. 3A & 3B). Together, the results of these studies support the Bayesian cue combination framework, in that: movement improves the precision of time perception not only in perceptual timing tasks but also motor timing tasks (Exp. 1A & 1B), stimulating the SMA appears to disrupt the transformation of temporal information (Exp. 2), and when movement becomes unreliable or noisy there is no longer an improvement in precision of time perception (Exp. 3A & 3B). Although there is support for the proposed framework, more studies (i.e., fMRI, TMS, EEG, etc.) need to be conducted in order to better understand where and how this may be instantiated in the brain; however, this work provides a starting point to better understanding the intrinsic connection between time and movement
Why is 7T MRI indispensable in epilepsy now?
Identifying a structural brain lesion on MRI is the most important factor that correlates with seizure freedom after surgery in patients suffering from drug-resistant focal epilepsy. By providing better image contrast and higher spatial resolution, structural MRI at 7 Tesla (7T) can lead to lesion detection in about 25% of patients presenting with negative MRI at lower fields. In addition to a better detection/delineation/phenotyping of epileptogenic lesions, higher signal at ultra-high field also facilitates more detailed analyses of several functional and molecular alterations of tissues, susceptible to detect epileptogenic properties even in absence of visible lesions. These advantages but also the technical challenges of 7T MRI in practice will be presented and discussed.
Dynamic endocrine modulation of the nervous system
Sex hormones are powerful neuromodulators of learning and memory. In rodents and nonhuman primates estrogen and progesterone influence the central nervous system across a range of spatiotemporal scales. Yet, their influence on the structural and functional architecture of the human brain is largely unknown. Here, I highlight findings from a series of dense-sampling neuroimaging studies from my laboratory designed to probe the dynamic interplay between the nervous and endocrine systems. Individuals underwent brain imaging and venipuncture every 12-24 hours for 30 consecutive days. These procedures were carried out under freely cycling conditions and again under a pharmacological regimen that chronically suppresses sex hormone production. First, resting state fMRI evidence suggests that transient increases in estrogen drive robust increases in functional connectivity across the brain. Time-lagged methods from dynamical systems analysis further reveals that these transient changes in estrogen enhance within-network integration (i.e. global efficiency) in several large-scale brain networks, particularly Default Mode and Dorsal Attention Networks. Next, using high-resolution hippocampal subfield imaging, we found that intrinsic hormone fluctuations and exogenous hormone manipulations can rapidly and dynamically shape medial temporal lobe morphology. Together, these findings suggest that neuroendocrine factors influence the brain over short and protracted timescales.
AI for Multi-centre Epilepsy Lesion Detection on MRI
Epilepsy surgery is a safe but underutilised treatment for drug-resistant focal epilepsy. One challenge in the presurgical evaluation of patients with drug-resistant epilepsy are patients considered “MRI negative”, i.e. where a structural brain abnormality has not been identified on MRI. A major pathology in “MRI negative” patients is focal cortical dysplasia (FCD), where lesions are often small or subtle and easily missed by visual inspection. In recent years, there has been an explosion in artificial intelligence (AI) research in the field of healthcare. Automated FCD detection is an area where the application of AI may translate into significant improvements in the presurgical evaluation of patients with focal epilepsy. I will provide an overview of our automated FCD detection work, the Multicentre Epilepsy Lesion Detection (MELD) project and how AI algorithms are beginning to be integrated into epilepsy presurgical planning at Great Ormond Street Hospital and elsewhere around the world. Finally, I will discuss the challenges and future work required to bring AI to the forefront of care for patients with epilepsy.
Multisensory processing of anticipatory and consummatory food cues
Visual Perception in Cerebral Visual Impairment (CVI)
A vision of numerical cognition
Modeling shared and variable information encoded in fine-scale cortical topographies
Information is encoded in fine-scale functional topographies that vary from brain to brain. Hyperalignment models information that is shared across brain in a high-dimensional common information space. Hyperalignment transformations project idiosyncratic individual topographies into the common model information space. These transformations contain topographic basis functions, affording estimates of how shared information in the common model space is instantiated in the idiosyncratic functional topographies of individual brains. This new model of the functional organization of cortex – as multiplexed, overlapping basis functions – captures the idiosyncratic conformations of both coarse-scale topographies, such as retinotopy and category-selectivity, and fine-scale topographies. Hyperalignment also makes it possible to investigate how information that is encoded in fine-scale topographies differs across brains. These individual differences in fine-grained cortical function were not accessible with previous methods.
Toward an open science ecosystem for neuroimaging
It is now widely accepted that openness and transparency are keys to improving the reproducibility of scientific research, but many challenges remain to adoption of these practices. I will discuss the growth of an ecosystem for open science within the field of neuroimaging, focusing on platforms for open data sharing and open source tools for reproducible data analysis. I will also discuss the role of the Brain Imaging Data Structure (BIDS), a community standard for data organization, in enabling this open science ecosystem, and will outline the scientific impacts of these resources.
Preclinical fMRI: Why should we care and what it's useful for
Representations of people in the brain
Faces and voices convey much of the non-verbal information that we use when communicating with other people. We look at faces and listen to voices to recognize others, understand how they are feeling, and decide how to act. Recent research in my lab aims to investigate whether there are similar coding mechanisms to represent faces and voices, and whether there are brain regions that integrate information across the visual and auditory modalities. In the first part of my talk, I will focus on an fMRI study in which we found that a region of the posterior STS exhibits modality-general representations of familiar people that can be similarly driven by someone’s face and their voice (Tsantani et al. 2019). In the second part of the talk, I will describe our recent attempts to shed light on the type of information that is represented in different face-responsive brain regions (Tsantani et al., 2021).
Driving human visual cortex, visually and electrically
The development of circuit-based therapeutics to treat neurological and neuropsychiatric diseases require detailed localization and understanding of electrophysiological signals in the human brain. Electrodes can record and stimulate circuits in many ways, and we often rely on non-invasive imaging methods to predict the location to implant electrodes. However, electrophysiological and imaging signals measure the underlying tissue in a fundamentally different manner. To integrate multimodal data and benefit from these complementary measurements, I will describe an approach that considers how different measurements integrate signals across the underlying tissue. I will show how this approach helps relate fMRI and intracranial EEG measurements and provides new insights into how electrical stimulation influences human brain networks.
It’s All About Motion: Functional organization of the multisensory motion system at 7T
The human middle temporal complex (hMT+) has a crucial biological relevance for the processing and detection of direction and speed of motion in visual stimuli. In both humans and monkeys, it has been extensively investigated in terms of its retinotopic properties and selectivity for direction of moving stimuli; however, only in recent years there has been an increasing interest in how neurons in MT encode the speed of motion. In this talk, I will explore the proposed mechanism of speed encoding questioning whether hMT+ neuronal populations encode the stimulus speed directly, or whether they separate motion into its spatial and temporal components. I will characterize how neuronal populations in hMT+ encode the speed of moving visual stimuli using electrocorticography ECoG and 7T fMRI. I will illustrate that the neuronal populations measured in hMT+ are not directly tuned to stimulus speed, but instead encode speed through separate and independent spatial and temporal frequency tuning. Finally, I will suggest that this mechanism may play a role in evaluating multisensory responses for visual, tactile and auditory stimuli in hMT+.
Trial by trial predictions of subjective time from human brain activity
Our perception of time isn’t like a clock; it varies depending on other aspects of experience, such as what we see and hear in that moment. However, in everyday life, the properties of these simple features can change frequently, presenting a challenge to understanding real-world time perception based on simple lab experiments. We developed a computational model of human time perception based on tracking changes in neural activity across brain regions involved in sensory processing, using fMRI. By measuring changes in brain activity patterns across these regions, our approach accommodates the different and changing feature combinations present in natural scenarios, such as walking on a busy street. Our model reproduces people’s duration reports for natural videos (up to almost half a minute long) and, most importantly, predicts whether a person reports a scene as relatively shorter or longer–the biases in time perception that reflect how natural experience of time deviates from clock time
Disentangling neural correlates of consciousness and task relevance using EEG and fMRI
How does our brain generate consciousness, that is, the subjective experience of what it is like to see face or hear a sound? Do we become aware of a stimulus during early sensory processing or only later when information is shared in a wide-spread fronto-parietal network? Neural correlates of consciousness are typically identified by comparing brain activity when a constant stimulus (e.g., a face) is perceived versus not perceived. However, in most previous experiments, conscious perception was systematically confounded with post-perceptual processes such as decision-making and report. In this talk, I will present recent EEG and fMRI studies dissociating neural correlates of consciousness and task-related processing in visual and auditory perception. Our results suggest that consciousness emerges during early sensory processing, while late, fronto-parietal activity is associated with post-perceptual processes rather than awareness. These findings challenge predominant theories of consciousness and highlight the importance of considering task relevance as a confound across different neuroscientific methods, experimental paradigms and sensory modalities.
Hierarchical transformation of visual event timing representations in the human brain: response dynamics in early visual cortex and timing-tuned responses in association cortices
Quantifying the timing (duration and frequency) of brief visual events is vital to human perception, multisensory integration and action planning. For example, this allows us to follow and interact with the precise timing of speech and sports. Here we investigate how visual event timing is represented and transformed across the brain’s hierarchy: from sensory processing areas, through multisensory integration areas, to frontal action planning areas. We hypothesized that the dynamics of neural responses to sensory events in sensory processing areas allows derivation of event timing representations. This would allow higher-level processes such as multisensory integration and action planning to use sensory timing information, without the need for specialized central pacemakers or processes. Using 7T fMRI and neural model-based analyses, we found responses that monotonically increase in amplitude with visual event duration and frequency, becoming increasingly clear from primary visual cortex to lateral occipital visual field maps. Beginning in area MT/V5, we found a gradual transition from monotonic to tuned responses, with response amplitudes peaking at different event timings in different recording sites. While monotonic response components were limited to the retinotopic location of the visual stimulus, timing-tuned response components were independent of the recording sites' preferred visual field positions. These tuned responses formed a network of topographically organized timing maps in superior parietal, postcentral and frontal areas. From anterior to posterior timing maps, multiple events were increasingly integrated, response selectivity narrowed, and responses focused increasingly on the middle of the presented timing range. These results suggest that responses to event timing are transformed from the human brain’s sensory areas to the association cortices, with the event’s temporal properties being increasingly abstracted from the response dynamics and locations of early sensory processing. The resulting abstracted representation of event timing is then propagated through areas implicated in multisensory integration and action planning.
The peripheral airways in Asthma: significance, assessment, and targeted treatment
The peripheral airways are technically challenging to assess and have been overlooked in the assessment of chronic respiratory diseases such as Asthma, in both the clinical and research space. Evidence of the importance of the small airways in Asthma is building, and small airways dysfunction is implicated in poor Asthma control, airway hyperresponsiveness, and exacerbation risk. The aim of this research was to complete comprehensive global, regional, and spatial assessments of airway function and ventilation in Asthma using physiological and MRI techniques. Specific ventilation imaging (SVI) and Phase resolved functional lung imaging (PREFUL) formed the spatial assessments. SVI uses oxygen as a contrast agent and looks at rate of change in signal to assess ventilation heterogeneity, PREFUL is a completely contrast free technique that uses Fourier decomposition to determine fractional ventilation.
A parsimonious description of global functional brain organization in three spatiotemporal patterns
Resting-state functional magnetic resonance imaging (MRI) has yielded seemingly disparate insights into large-scale organization of the human brain. The brain’s large-scale organization can be divided into two broad categories: zero-lag representations of functional connectivity structure and time-lag representations of traveling wave or propagation structure. In this study, we sought to unify observed phenomena across these two categories in the form of three low-frequency spatiotemporal patterns composed of a mixture of standing and traveling wave dynamics. We showed that a range of empirical phenomena, including functional connectivity gradients, the task-positive/task-negative anti-correlation pattern, the global signal, time-lag propagation patterns, the quasiperiodic pattern and the functional connectome network structure, are manifestations of these three spatiotemporal patterns. These patterns account for much of the global spatial structure that underlies functional connectivity analyses and unifies phenomena in resting-state functional MRI previously thought distinct.
Multi-level theory of neural representations in the era of large-scale neural recordings: Task-efficiency, representation geometry, and single neuron properties
A central goal in neuroscience is to understand how orchestrated computations in the brain arise from the properties of single neurons and networks of such neurons. Answering this question requires theoretical advances that shine light into the ‘black box’ of representations in neural circuits. In this talk, we will demonstrate theoretical approaches that help describe how cognitive and behavioral task implementations emerge from the structure in neural populations and from biologically plausible neural networks. First, we will introduce an analytic theory that connects geometric structures that arise from neural responses (i.e., neural manifolds) to the neural population’s efficiency in implementing a task. In particular, this theory describes a perceptron’s capacity for linearly classifying object categories based on the underlying neural manifolds’ structural properties. Next, we will describe how such methods can, in fact, open the ‘black box’ of distributed neuronal circuits in a range of experimental neural datasets. In particular, our method overcomes the limitations of traditional dimensionality reduction techniques, as it operates directly on the high-dimensional representations, rather than relying on low-dimensionality assumptions for visualization. Furthermore, this method allows for simultaneous multi-level analysis, by measuring geometric properties in neural population data, and estimating the amount of task information embedded in the same population. These geometric frameworks are general and can be used across different brain areas and task modalities, as demonstrated in the work of ours and others, ranging from the visual cortex to parietal cortex to hippocampus, and from calcium imaging to electrophysiology to fMRI datasets. Finally, we will discuss our recent efforts to fully extend this multi-level description of neural populations, by (1) investigating how single neuron properties shape the representation geometry in early sensory areas, and by (2) understanding how task-efficient neural manifolds emerge in biologically-constrained neural networks. By extending our mathematical toolkit for analyzing representations underlying complex neuronal networks, we hope to contribute to the long-term challenge of understanding the neuronal basis of tasks and behaviors.
Neuroscience of socioeconomic status and poverty: Is it actionable?
SES neuroscience, using imaging and other methods, has revealed generalizations of interest for population neuroscience and the study of individual differences. But beyond its scientific interest, SES is a topic of societal importance. Does neuroscience offer any useful insights for promoting socioeconomic justice and reducing the harms of poverty? In this talk I will use research from my own lab and others’ to argue that SES neuroscience has the potential to contribute to policy in this area, although its application is premature at present. I will also attempt to forecast the ways in which practical solutions to the problems of poverty may emerge from SES neuroscience. Bio: Martha Farah has conducted groundbreaking research on face and object recognition, visual attention, mental imagery, and semantic memory and - in more recent times - has been at the forefront of interdisciplinary research into neuroscience and society. This deals with topics such as using fMRI for lie detection, ethics of cognitive enhancement, and effects of social deprivation on brain development.
Online Training of Spiking Recurrent Neural Networks With Memristive Synapses
Spiking recurrent neural networks (RNNs) are a promising tool for solving a wide variety of complex cognitive and motor tasks, due to their rich temporal dynamics and sparse processing. However training spiking RNNs on dedicated neuromorphic hardware is still an open challenge. This is due mainly to the lack of local, hardware-friendly learning mechanisms that can solve the temporal credit assignment problem and ensure stable network dynamics, even when the weight resolution is limited. These challenges are further accentuated, if one resorts to using memristive devices for in-memory computing to resolve the von-Neumann bottleneck problem, at the expense of a substantial increase in variability in both the computation and the working memory of the spiking RNNs. In this talk, I will present our recent work where we introduced a PyTorch simulation framework of memristive crossbar arrays that enables accurate investigation of such challenges. I will show that recently proposed e-prop learning rule can be used to train spiking RNNs whose weights are emulated in the presented simulation framework. Although e-prop locally approximates the ideal synaptic updates, it is difficult to implement the updates on the memristive substrate due to substantial device non-idealities. I will mention several widely adapted weight update schemes that primarily aim to cope with these device non-idealities and demonstrate that accumulating gradients can enable online and efficient training of spiking RNN on memristive substrates.
The glymphatic system in motor neurone disease
Neurodegenerative diseases are chronic and inexorable conditions characterised by the presence of insoluble aggregates of abnormally ubiquinated and phosphorylated proteins. Recent evidence also suggests that protein misfolding can propagate throughout the body in a prion-like fashion via the interstitial or cerebrospinal fluids (CSF). As protein aggregation occurs well before the onset of brain damage and symptoms, new biomarkers sensitive to early pathology, together with therapeutic strategies that include eliminating seed proteins and blocking cell-to-cell spread, are of vital importance. The glymphatic system, which facilitates the continuous exchange of CSF and interstitial fluid to clear the brain of waste, presents as a potential biomarker of disease severity, therapeutic target, and drug delivery system. In this webinar, Associate Professor David Wright from the Department of Neuroscience, Monash University, will outline recent advances in using MRI to investigate the glymphatic system. He will also present some of his lab’s recent work investigating glymphatic clearance in preclinical models of motor neurone disease. Associate Professor David Wright is an NHMRC Emerging Leadership Fellow and the Director of Preclinical Imaging in the Department of Neuroscience, Monash University and the Alfred Research Alliance, Alfred Health. His research encompasses the development, application and analysis of advanced magnetic resonance imaging techniques for the study of disease, with a particular emphasis on neurodegenerative disorders. Although less than three years post PhD, he has published over 60 peer-reviewed journal articles in leading neuroscience journals such as Nature Medicine, Brain, and Cerebral Cortex.
CNStalk: Mapping brain function with ultra-high field MRI
Chemistry of the adaptive mind: lessons from dopamine
The human brain faces a variety of computational dilemmas, including the flexibility/stability, the speed/accuracy and the labor/leisure tradeoff. I will argue that striatal dopamine is particularly well suited to dynamically regulate these computational tradeoffs depending on constantly changing task demands. This working hypothesis is grounded in evidence from recent studies on learning, motivation and cognitive control in human volunteers, using chemical PET, psychopharmacology, and/or fMRI. These studies also begin to elucidate the mechanisms underlying the huge variability in catecholaminergic drug effects across different individuals and across different task contexts. For example, I will demonstrate how effects of the most commonly used psychostimulant methylphenidate on learning, Pavlovian and effortful instrumental control depend on fluctuations in current environmental volatility, on individual differences in working memory capacity and on opportunity cost respectively.
The neural basis of flexible semantic cognition (BACN Mid-career Prize Lecture 2022)
Semantic cognition brings meaning to our world – it allows us to make sense of what we see and hear, and to produce adaptive thoughts and behaviour. Since we have a wealth of information about any given concept, our store of knowledge is not sufficient for successful semantic cognition; we also need mechanisms that can steer the information that we retrieve so it suits the context or our current goals. This talk traces the neural networks that underpin this flexibility in semantic cognition. It draws on evidence from multiple methods (neuropsychology, neuroimaging, neural stimulation) to show that two interacting heteromodal networks underpin different aspects of flexibility. Regions including anterior temporal cortex and left angular gyrus respond more strongly when semantic retrieval follows highly-related concepts or multiple convergent cues; the multivariate responses in these regions correspond to context-dependent aspects of meaning. A second network centred on left inferior frontal gyrus and left posterior middle temporal gyrus is associated with controlled semantic retrieval, responding more strongly when weak associations are required or there is more competition between concepts. This semantic control network is linked to creativity and also captures context-dependent aspects of meaning; however, this network specifically shows more similar multivariate responses across trials when association strength is weak, reflecting a common controlled retrieval state when more unusual associations are the focus. Evidence from neuropsychology, fMRI and TMS suggests that this semantic control network is distinct from multiple-demand cortex which supports executive control across domains, although challenging semantic tasks recruit both networks. The semantic control network is juxtaposed between regions of default mode network that might be sufficient for the retrieval of strong semantic relationships and multiple-demand regions in the left hemisphere, suggesting that the large-scale organisation of flexible semantic cognition can be understood in terms of cortical gradients that capture systematic functional transitions that are repeated in temporal, parietal and frontal cortex.
Growing a world-class precision medicine industry
Monash Biomedical Imaging is part of the new $71.2 million Australian Precision Medicine Enterprise (APME) facility, which will deliver large-scale development and manufacturing of precision medicines and theranostic radiopharmaceuticals for industry and research. A key feature of the APME project is a high-energy cyclotron with multiple production clean rooms, which will be located on the Monash Biomedical Imaging (MBI) site in Clayton. This strategic co-location will facilitate radiochemistry, PET and SPECT research and clinical use of theranostic (therapeutic and diagnostic) radioisotopes produced on-site. In this webinar, MBI’s Professor Gary Egan and Dr Maggie Aulsebrook will explain how the APME will secure Australia’s supply of critical radiopharmaceuticals, build a globally competitive Australian manufacturing hub, and train scientists and engineers for the Australian workforce. They will cover the APME’s state-of-the-art 30 MeV and 18-24 MeV cyclotrons and radiochemistry facilities, as well as the services that will be accessible to students, scientists, clinical researchers, and pharmaceutical companies in Australia and around the world. The APME is a collaboration between Monash University, Global Medical Solutions Australia, and Telix Pharmaceuticals. Professor Gary Egan is Director of Monash Biomedical Imaging, Director of the ARC Centre of Excellence for Integrative Brain Function and a Distinguished Professor at the Turner Institute for Brain and Mental Health, Monash University. He is also lead investigator of the Victorian Biomedical Imaging Capability, and Deputy Director of the Australian National Imaging Facility. Dr Maggie Aulsebrook obtained her PhD in Chemistry at Monash University and specialises in the development and clinical translation of radiopharmaceuticals. She has led the development of several investigational radiopharmaceuticals for first-in-human application. Maggie leads the Radiochemistry Platform at Monash Biomedical Imaging.
Can I be bothered? Neural and computational mechanisms underlying the dynamics of effort processing (BACN Early-career Prize Lecture 2021)
From a workout at the gym to helping a colleague with their work, everyday we make decisions about whether we are willing to exert effort to obtain some sort of benefit. Increases in how effortful actions and cognitive processes are perceived to be has been linked to clinically severe impairments to motivation, such as apathy and fatigue, across many neurological and psychiatric conditions. However, the vast majority of neuroscience research has focused on understanding the benefits for acting, the rewards, and not on the effort required. As a result, the computational and neural mechanisms underlying how effort is processed are poorly understood. How do we compute how effortful we perceive a task to be? How does this feed into our motivation and decisions of whether to act? How are such computations implemented in the brain? and how do they change in different environments? I will present a series of studies examining these questions using novel behavioural tasks, computational modelling, fMRI, pharmacological manipulations, and testing in a range of different populations. These studies highlight how the brain represents the costs of exerting effort, and the dynamic processes underlying how our sensitivity to effort changes as a function of our goals, traits, and socio-cognitive processes. This work provides new computational frameworks for understanding and examining impaired motivation across psychiatric and neurological conditions, as well as why all of us, sometimes, can’t be bothered.
ItsAllAboutMotion: Encoding of speed in the human Middle Temporal cortex
The human middle temporal complex (hMT+) has a crucial biological relevance for the processing and detection of direction and speed of motion in visual stimuli. In both humans and monkeys, it has been extensively investigated in terms of its retinotopic properties and selectivity for direction of moving stimuli; however, only in recent years there has been an increasing interest in how neurons in MT encode the speed of motion. In this talk, I will explore the proposed mechanism of speed encoding questioning whether hMT+ neuronal populations encode the stimulus speed directly, or whether they separate motion into its spatial and temporal components. I will characterize how neuronal populations in hMT+ encode the speed of moving visual stimuli using electrocorticography ECoG and 7T fMRI. I will illustrate that the neuronal populations measured in hMT+ are not directly tuned to stimulus speed, but instead encode speed through separate and independent spatial and temporal frequency tuning. Finally, I will show that this mechanism plays a role in evaluating multisensory responses for visual, tactile and auditory motion stimuli in hMT+.
MBI Webinar on preclinical research into brain tumours and neurodegenerative disorders
WEBINAR 1 Breaking the barrier: Using focused ultrasound for the development of targeted therapies for brain tumours presented by Dr Ekaterina (Caty) Salimova, Monash Biomedical Imaging Glioblastoma multiforme (GBM) - brain cancer - is aggressive and difficult to treat as systemic therapies are hindered by the blood-brain barrier (BBB). Focused ultrasound (FUS) - a non-invasive technique that can induce targeted temporary disruption of the BBB – is a promising tool to improve GBM treatments. In this webinar, Dr Ekaterina Salimova will discuss the MRI-guided FUS modality at MBI and her research to develop novel targeted therapies for brain tumours. Dr Ekaterina (Caty) Salimova is a Research Fellow in the Preclinical Team at Monash Biomedical Imaging. Her research interests include imaging cardiovascular disease and MRI-guided focused ultrasound for investigating new therapeutic targets in neuro-oncology. - WEBINAR 2 Disposition of the Kv1.3 inhibitory peptide HsTX1[R14A], a novel attenuator of neuroinflammation presented by Sanjeevini Babu Reddiar, Monash Institute of Pharmaceutical Sciences The voltage-gated potassium channel (Kv1.3) in microglia regulates membrane potential and pro-inflammatory functions, and non-selective blockade of Kv1.3 has shown anti-inflammatory and disease improvement in animal models of Alzheimer’s and Parkinson’s diseases. Therefore, specific inhibitors of pro-inflammatory microglial processes with CNS bioavailability are urgently needed, as disease-modifying treatments for neurodegenerative disorders are lacking. In this webinar, PhD candidate Ms Sanju Reddiar will discuss the synthesis and biodistribution of a Kv1.3-inhibitory peptide using a [64Cu]Cu-DOTA labelled conjugate. Sanjeevini Babu Reddiar is a PhD student at the Monash Institute of Pharmaceutical Sciences. She is working on a project identifying the factors governing the brain disposition and blood-brain barrier permeability of a Kv1.3-blocking peptide.
Signatures of fractal temporal dependencies are correlated between MEG and fMRI
Bernstein Conference 2024
Towards predicting Stroke Etiology from MRI and CT Imaging Data of Ischemic Stroke Patients
Bernstein Conference 2024
Individualized representation learning of resting-state fMRI
COSYNE 2023
Evidence for compositionality in fMRI visual representations
COSYNE 2025
fMRI study reveals enhanced top-down and bottom-up processes in schizophrenia
COSYNE 2025
Analyzing activity-dependent gene plasticity using a genetic reporter for MRI
FENS Forum 2024
Awake rat MRI scanning - A contribution to the AwakeRodent multi-center, multi-species, multi-modality study
FENS Forum 2024
Benchmarking deep-learning based whole-brain MRI segmentation tools for morphometry
FENS Forum 2024
Changes in the amplitude of the task-evoked hemodynamic response during grip movements; simultaneous fNIRS and fMRI measurements
FENS Forum 2024
Cognitive map formation and virtual navigation in blind subjects: An fMRI study
FENS Forum 2024
Comparison of SynthSeg performance between 3T and 7T MRI in MR-negative epilepsy
FENS Forum 2024
A connectome-based fMRI study of spatial reasoning in stroke
FENS Forum 2024
Coupling between global grey matter and fourth ventricle fMRI signals links with brain clearance in humans
FENS Forum 2024
Deciphering the role of locus coeruleus through salient stimulus detection using functional MRI
FENS Forum 2024
Decoding of fMRI resting-state using task-based MVPA supports the Incentive-Sensitization Theory in smokers
FENS Forum 2024
Early microstructural alterations in Alzheimer’s disease: novel MRI biomarkers of Aß deposition and glial activation in APP/PS1 mouse model
FENS Forum 2024
Effects of performance and additional punishment on auditory-evoked brain activation patterns in discrimination learning – An auditory fMRI study in the Mongolian gerbil
FENS Forum 2024
Environment for precise EEG electrode localization on data from low-cost structured light projector cameras or MRI head scans
FENS Forum 2024
fMRI mapping of brain circuits during simple sound perception by awake rats
FENS Forum 2024
Functional and microstructural MRI substrates of conserved memory in healthy ageing
FENS Forum 2024
Functional MRI of sleeping pigeons
FENS Forum 2024
GPT-4 can recognize Theory of Mind in natural conversations: fMRI evidence
FENS Forum 2024
High-resolution fMRI reveals an extensive cortical network responding to conspecific emotional vocalisations in macaques
FENS Forum 2024
The inside-out of emotion processing: Evaluating children and adults’ neural correlates from a novel fMRI movie-watching paradigm
FENS Forum 2024
Introducing Psy-ShareD (Psychosis MRI Shared Data Resource): A new global MRI repository for all psychosis researchers
FENS Forum 2024
Investigating reward-related memory enhancement in ascending arousal system nuclei using 7T MRI
FENS Forum 2024
Investigating strategies to account gender differences in mental rotation tasks - An fMRI study
FENS Forum 2024
A labeled clinical-MRI dataset of Nigerian brains
FENS Forum 2024
M1-PMd connectivity modulation via fMRI-neurofeedback
FENS Forum 2024
V1 makes the dominant contribution to the steady-state visual evoked potential: Evidence from retinotopically varying EEG topographies and MRI-derived forward models
FENS Forum 2024
Mapping social cognition in patients with gliomas: Preoperative and intraoperative insights from fMRI, MEG, and direct electrical stimulation
FENS Forum 2024
MRI-visible superparamagnetic ultraflexible electrodes for precision electrophysiology
FENS Forum 2024
Narrowband fMRI BOLD signal entropy predicts neonatal age
FENS Forum 2024
Neural dynamics of mood-influenced driving using fMRI: Connectivity patterns and speed variations
FENS Forum 2024
Neurovascular coupling along the optic nerve: Insights from two-photon imaging, functional ultrasound, and high-resolution BOLD fMRI
FENS Forum 2024
A novel MRI-compatible restrain setup for awake rat multimodal experiments
FENS Forum 2024
Observation of social and non-social interactions in dogs and humans: Results from fMRI and eyetracking
FENS Forum 2024
Oculomotor vergence system through fMRI in persons with binocularly normal vision and persistent post-concussive symptoms with convergence insufficiency
FENS Forum 2024
OptoSens-fMRI of the nigrostriatal pathway
FENS Forum 2024
Pre-operative structural MRI predicts cochlear therapy outcome in post-lingual deafness
FENS Forum 2024