Neurosalience #S6E5 with Ahmed Khalil - BOLD delay mapping for stroke perfusion imaging

“Naturalistic stimuli open up new exploration…”Dr. Christopher Baldassano is an associate professor at Columbia University and leads the Dynamic Perception and Memory Lab. With a background in electrical engineering from Princeton and a PhD in computer science from Stanford, Chris has pioneered innovative approaches to understanding memory and cognition. Following a postdoc at Princeton with Uri Hasson and Ken Norman, he joined Columbia in 2018. His research focuses on how the brain processes, stores, and retrieves events using naturalistic stimuli, hidden Markov models, and multivariate analysis techniques.In this episode, Peter and Chris explore the fascinating world of event structures and memory. They discuss Chris’s pioneering work on event scripts, neural frameworks that act as cognitive scaffolds for autobiographical memories. The conversation covers how the brain segments continuous experience into discrete events, the role of event boundaries in memory encoding, and the critical function of the hippocampus in organizing these temporal structures. Chris explains his use of naturalistic stimuli and hidden Markov models to reveal the subtle dynamics of how we combine recurring information to respond more efficiently to future experiences. Along the way, Chris shares valuable insights on the evolution of neuroscience research and offers thoughtful advice for aspiring scientists navigating the field.We hope you enjoy this episode!Chapters:00:00 - Introduction07:37 - Transitioning from Computer Science to Neuroscience13:01 - Exploring Naturalistic Stimuli in Neuroscience18:11 - Hidden Markov Models in Narrative Perception22:46 - Event Boundaries and Memory Encoding27:49 - The Role of the Hippocampus in Memory33:01 - Implications for Mental Health and Memory Disorders38:19 - Enhancing Memory Techniques41:11 - Contextualization in Memory46:19 - Understanding Brain States49:01 - AI and Contextual Knowledge53:29 - Infant Cognition and Event Structures01:01:31 - Future Directions in ResearchWorks mentioned:2:28 - https://www.youtube.com/watch?v=jPLWOBmaLkY(Baldassano talk at NIH workshop on naturalistic stimuli)14:42 - https://pubmed.ncbi.nlm.nih.gov/28772125/(Baldassano et al., 2017 - Neuron - "Discovering Event Structure in Continuous Narrative Perception and Memory")15:02 - https://pubmed.ncbi.nlm.nih.gov/30249790/(Baldassano et al., 2018 - Journal of Neuroscience - "Representation of Real-world Event Schemas During Narrative Perception")18:24 - https://pubmed.ncbi.nlm.nih.gov/29087305/(Vidaurre, Smith & Woolrich, 2017 - PNAS - "Brain network dynamics are hierarchically organized in time" - using Markov models in a different way)19:41 - https://pubmed.ncbi.nlm.nih.gov/17338600/(Zacks et al., 2007 - Psychological Bulletin - "Event perception: A mind-brain perspective" - foundational work on event boundary processes)27:04 - https://pubmed.ncbi.nlm.nih.gov/27121839/(Huth et al., 2016 - Nature - "Natural speech reveals the semantic maps that tile human cerebral cortex" - semantic information stored throughout the brain)37:15 - https://pubmed.ncbi.nlm.nih.gov/22982082/(LePort et al., 2012 - Neurobiology of Learning and Memory - Jim McGaugh's study on highly superior autobiographical memory)53:01 - https://pubmed.ncbi.nlm.nih.gov/36252007/(Yates et al., 2022 - PNAS - "Neural event segmentation of continuous experience in human infants")Episode producers:Xuqian Michelle Li

Dr. Ahmed Khalil is an MD-PhD currently serving his residency in radiology at the Institute of Neuroradiology at Charité University Hospital in Berlin. Originally from Sudan, he has been doing pioneering work on resting-state BOLD latency mapping, a technique that reveals flow deficits in the brain associated with stroke. His research demonstrates that this approach compares favorably with the current clinical gold standard of dynamic susceptibility contrast imaging using gadolinium, while capturing useful data in as little as two minutes.In this episode, Peter and Ahmed discuss his work translating advanced MRI techniques into clinical practice. They explore how BOLD latency mapping can detect perfusion deficits and compare with both traditional gadolinium-based methods and DTI for identifying stroke lesions. The conversation delves into the broader challenge faced by all promising research methods: what does it actually take to move from successful proof-of-concept to daily clinical practice on scanners around the world?Ahmed and Peter also talk about the cultural gap between research-level image processing and the clinical preference for minimally processed, interpretable data and how AI might help bridge that divide. Along the way, Ahmed shares valuable advice for MD-PhD students on the importance of collaboration, learning from diverse experts, and maintaining curiosity across disciplines.We hope you enjoy this episode!Chapters:00:00 - Introduction to Ahmed Khalil and His Work05:02 - Journey into Medicine and Radiology12:10 - The Challenges of Methods Development in Clinical Applications22:15 - Research on Resting State BOLD Latency37:27 - Clinical Implications of Perfusion Imaging in Stroke43:52 - Challenges in Clinical Implementation of New Imaging Techniques47:50 - The Role of AI in Radiology and Imaging Interpretation52:42 - Future Aspirations and Research Directions in Imaging01:01:03 - Collaborative Efforts in Physiologic MRI Book Project01:03:25 - Advice for Aspiring MD-PhD StudentsWorks mentioned:22:48 - https://pubmed.ncbi.nlm.nih.gov/23378326/(Lv et al., 2013 - First paper showing BOLD delay in stroke with Arno Villinger)23:08 - https://www.ahajournals.org/doi/10.1161/STROKEAHA.116.015566(Khalil et al., 2017 - Stroke paper, Relationship between BOLD delay and DSC-MRI)23:08 - https://pubmed.ncbi.nlm.nih.gov/30334657/(Khalil et al., 2018 - JCBFM paper, Longitudinal changes in BOLD delay)39:00 - https://pubmed.ncbi.nlm.nih.gov/34323339/(Hu et al., 2021 - Human Brain Mapping paper with Daniel Margulies - ICA approach)Episode producers:Ömer Faruk Gülban, Xuqian Michelle Li

“What makes certain brain networks vulnerable to disease—and can AI help us predict what comes next?”Dr. Juan Helen Zhou is a computational neuroscientist at the National University of Singapore, where she is an Associate Professor and Director of the Center for Translational Magnetic Resonance Research at the Yong Loo Lin School of Medicine. She leads the Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory, integrating multimodal brain imaging and machine learning to study network vulnerability in aging and neuropsychiatric disorders, including dementia, psychosis, and ADHD.In this episode, Peter and Helen discuss her path from computer science to neuroscience and how that background shaped her approach to brain imaging and AI. They explore her work on dementia, including the role of cerebral vascular disease, why different forms of dementia must be understood as distinct network-level disorders, and how selective brain network vulnerabilities can predict cognitive decline.The discussion also covers recent advances from Dr. Zhou’s lab in reconstructing images from brain activity using generative AI and self-supervised learning, highlighting both the promise and challenges of these approaches. Along the way, Helen reflects on the importance of collaboration in neuroscience and shares advice for early-career researchers on persistence, communication, and navigating interdisciplinary science.We hope you enjoy this episode!Chapters:00:00 - Introduction to Helen Zhou and Her Background03:28 - Journey from Computer Science to Neuroscience11:13 - The Center for Translational MR Research12:59 - Involvement with OHBM and Community Growth23:44 - Research Focus on Dementia and Brain Networks28:05 - Exploring Cerebral Vasculitis and Dementia Stages44:02 - Functional Specialization and Cognitive Performance45:34 - AI-Based Interventions for Cognitive Health58:30 - Utilizing Large Datasets for Brain Research01:08:53 - Advice for Aspiring NeuroscientistsWorks mentioned:25:18 - https://www.cell.com/neuron/fulltext/S0896-6273(09)00249-925:18 - https://www.cell.com/neuron/fulltext/S0896-6273(12)00227-926:55 - https://www.neurology.org/doi/10.1212/WNL.000000000000831538:33 - https://www.neurology.org/doi/10.1212/wnl.000000000020740141:00 - https://www.sciencedirect.com/science/article/abs/pii/S105381191600234242:33 - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.007941947:46 - https://openaccess.thecvf.com/content/CVPR2023/html/Chen_Seeing_Beyond_the_Brain_Conditional_Diffusion_Model_With_Sparse_Masked_CVPR_2023_paper.html55:11 - https://www.nature.com/articles/s41586-022-04554-yEpisode producers:Karthik Sama, Xuqian Michelle Li

“What does it actually mean to understand the brain?”Dr. Kendrick Kay is a computational neuroscientist and neuroimaging expert at the University of Minnesota’s Center for Magnetic Resonance Research, where he is an Associate Professor in the Department of Radiology. With training spanning philosophy and neuroscience, from a bachelor’s degree in philosophy at Harvard University to a PhD in neuroscience from UC Berkeley, Dr. Kay’s work bridges deep theoretical questions with cutting-edge neuroimaging methods.In this conversation, Peter Bandettini and Kendrick Kay explore the evolving landscape of neuroscience at the intersection of fMRI, philosophy, and artificial intelligence. They reflect on the limits of current neuroimaging methodologies, what fMRI can and cannot tell us about brain mechanisms, and why creativity and human judgment remain central to scientific progress. The discussion also dives into Dr. Kay’s landmark contributions to fMRI decoding and the Natural Scenes Dataset, a high-resolution resource that has become foundational for computational neuroscience and neuro AI research.Along the way, they examine deep sampling in neuroimaging, individual variability in brain data, and the challenges of separating neural signals from hemodynamic effects. Framed by broader questions about understanding benchmarking progress, and the growing role of LLM’s in neuroscience, this wide-ranging conversation offers a thoughtful look at where the field has been and where it may be headed.We hope you enjoy this episode!Chapters:00:00 - Introduction to Kendrick Kay and His Work04:51 - Philosophy’s Influence on Neuroscience17:17 - How Far Will fMRI Take Us?23:27 - Understanding Attention in Neuroscience30:00 - Science as a Process34:17 - The Role of Large Language Models (LLMs) in Scientific Progress38:29 - Why Humans Should Stay in the Equation40:30 - Creativity vs. AI in Scientific Research54:48 - Dr. Kay’s Natural Scenes Dataset (NSD)01:00:27 - Deep Sampling: Considerations and Implications01:08:00 - Accounting for biological variation in Brain Scans: Differences and Similarities01:13:00 - Separating Hemodynamic Effects from Neural Effects01:16:00 - Areas of Hope and Progress in the field01:21:00 - How Should We Benchmark Progress?01:22:59 - Advice for Aspiring ScientistsWorks mentioned:54:48 -  https://www.nature.com/articles/s41593-021-00962-x54:50 - https://www.sciencedirect.com/science/article/pii/S0166223624001838?via%3DihubEpisode producers:Xuqian Michelle Li, Naga Thovinakere

"AI is really bad at perspective taking…"Dr. Charlotte Grosse Wiesmann is a cognitive neuroscientist exploring how the human social brain takes shape in early life. She is a Professor at the University of Technology Nuremberg and directs the Research Group on Social Brain Development at the Max Planck Institute in Leipzig. Her research blends developmental psychology, brain imaging, and computational modeling to uncover how infants begin to infer other people’s beliefs, intentions and mental states. In this conversation, Dr. Wiesmann unpacks how children’s brains develop the capacity for social understanding and theory of mind. Drawing on developmental psychology and neuroimaging, she reveals how the brain transforms as children first succeed on false-belief tasks, a fleeting yet powerful window into the emergence of the social mind. Within this context, the conversation explores white matter maturation, environmental influences, and brain plasticity, offering fresh insights into how studying infant development can inform the future of AI. Join the conversation to discover how early brain development is reshaping our understanding of our social minds.We hope you enjoy this episode!Chapters:00:00 - A Journey from Physics to Neuroscience14:25 - Neural Bases of Early Childhood Theory of Mind21:58 - False Belief Task and Theory of Mind25:11 - Attention Schema for Consciousness27:14 - Primary Areas Involved in Theory of Mind31:24 - Impact of Neuro Deficits on Social Cognition33:57 - Role of Environment and Timing on Social Cognition37:11 - Implicit and Explicit Mechanisms of Social Development45:02 - Social Cognition Across Species47:37 - Connecting Neural Code to Social Cognition49:56 - Temporal Progression in Theory of Mind Tasks54:54 - Future Research Directions in Understanding Social Cognition01:00:08 - Infant Learning Inspires AI Development01:04:50 - Advice for Aspiring ScientistsWorks mentioned:14:31 -  White matter maturation is associated with the emergence of Theory of Mind in early childhood37:20 -  Two systems for thinking about others’ thoughts in the developing brain49:50 -  Timing matters: disentangling the neurocognitive sequence of mentalizingEpisode producers:Xuqian Michelle Li, Karthik Sama

"I really enjoy good conversations..."In this episode, we look back at the highlights from last season and share some fun insights from our audience metrics. We’re celebrating six years of Neurosalience, and we’re excited for the incredible guests and topics coming up this season.We hope you enjoy this episode!Chapters:00:00 - Introduction to season 601:43 - Highlights from season 507:55 - Reflections on the podcast's impact20:36 - Discussion on the DIANA paper retraction27:21 - Upcoming guests and topics32:04 - Innovations for season 6Episode producer:Xuqian Michelle Li

Early career researchers give their perspectives on being an academic today. With Arshiya  Sangchooli, Natasha L. Taylor, Ashlea Segal, Stefano Moia, Jiajia Yang, and Peter Bandettini Episode ProducersOmer Faruk GulbanXuqian Michelle Li

Peter Bandettini interviews Dr. Rosanna Olsen, a senior scientist at the Rotman Research Institute and the University of Toronto. She is pioneering what we know about human memory and its associated structures, primarily focusing on the hippocampus, the role it plays, and how it changes with age and neurological diseases. Her work has shed light on how the hippocampus facilitates the flexible binding and comparison of new and existing information. She has also shown how visual exploration reveals memory processes, and has uncovered promising early dementia biomarkers based on measures of visual exploration and hippocampus. Dr. Olsen is also a leader in education. She is co-lead of the Research Training Center in Toronto, disseminating essential knowledge and skills to younger scientists, and is chair-elect of the OHBM education committee. She is also the leader of a consortium organized to reach a consensus on hippocampus segmentation. Lastly she's an avid and accomplished runner, having run the Boston Marathon, as well as many others.We hope you enjoy the conversation! Episode ProducersOmer Faruk GulbanXuqian Michelle Li

This OHBM preview podcast offers an in-depth look at how the OHBM Annual Meeting is organized, along with reflections on the unique character of the meeting and the broader OHBM community. Peter Bandettini hosts Jean Chen, Marta Garrido, and Lena Oestreich, with Kevin Sitek serving as co-host. Michael Breakspear joins the discussion in the final 20 minutes. The conversation covers both logistical and thematic aspects of the meeting, providing valuable context for attendees and those interested in the field.Episode ProducersXuqian Michelle LiKarthik Sama

In this episode Peter Bandettini, Nikolaus Kriegeskorte, Aina Puce and Michael Breakspear discuss the future of scientific publishing.Episode ProducersOmer Faruk GulbanXuqian Michelle Li