Merge pull request #135 from Brainhack-Donostia/BHD2024

Bhd2024

Author: ihintza

_posts/2023-09-22-project-1.markdown

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+title: Programming transparency - Introduction to GitHub
+subtitle: "Marco Flores-Coronado - PhD Student @ Basque Center on Cognition, Brain and Language"
+layout: default
+modal-id: 1
+date: 2024-11-25
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+thumbnail: 
+alt: image-alt
+project-date: November 2024
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+category:
+description: "Marco completed his bachelor studies in Hispanic Philology and Literature at the National Autonomous University of Mexico. There, he carried out his own research project funded by the Psychology School regarding reading abilities in children with Autism Spectrum Disorder and eyetracking. Afterwards, he completed an MSc in Computational Modeling and Scientific Calculus with a specialization in robotics at the Autonomous University of Morelos State (UAEM), Mexico. During this period, he developed a computer model that simulated Cortical connections between different brain areas, and that accounts for audiovisual integration during speech perception. Soon after, he won a Caixa INPhINIT doctoral grant to continue his studies with a PhD in Cognitive Neurosciences at the Basque Center on Cognition Brain and Language (BCBL) and the University of the Basque Country (UPV-EHU) within the Signal Processing in Neuroimaging research group, and the Speech and Bilingualism group. Currently, he is developing analysis methods to improve MRI signal quality during overt speech production experiments. This will hinder investigation in speech production with MRI. His research interest is language processing but he follows a multidisciplinary perspective including tools from robotics, signal engineering, cognitive sciences, and computer science."
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+abstract: "There is a strong will within the research community for open science. Git repositories have become a tool for democratizing analysis pipelines, scientific software, and resource sharing. Moreover, Git allows researchers and developers to have transparency in their research methodology, with the potential for collaboration and community building besides frontiers. During this event, we will talk about the relevance of open-sourcing code while aiming to teach Git essential tools alongside the GitHub platform. Attendees will learn the basic Git workflow, Git commands, branching, undoing changes, and forking. All these tools will be useful for beginners and more experienced people during the hands-on projects part of BrainHack Donostia 2024."
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_posts/2023-09-22-project-2.markdown

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+title: Standardizing Neuroimaging Data - Introduction to Brain Imaging Data Structure (BIDS)
+subtitle: "David Carcedo - Lab Section Coordinator (MRI & behavioral) @  Basque Center on Cognition, Brain and Language \ Ryland Miller - Research Assistant @ Basque Center on Cognition, Brain and Language"
+layout: default
+modal-id: 3
+date: 2024-11-26
+img: 
+thumbnail: 
+alt: image-alt
+project-date: November 2025
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+category: 
+description: " David holds a degree in Psychology from the University of the Basque Country (UPV). Additionally, he is a certified technician in diagnostic imaging and nuclear medicine (Inmakulada Tolosa). With 12 years of experience as a laboratory technician at the Basque Center on Cognition, Brain, and Language (BCBL), he serves as the MRI Coordinator at BCBL. During his master’s thesis (Universitat de Valencia), he worked extensively on converting a multimodal dataset from a BCBL project into BIDS format. This has involved magnetic resonance imaging (MRI) data, electroencephalography (EEG) data, neuropsychological questionnaires, and medical information collected over multiple time points and across three different treatment groups. \\ Ryland received his Bachelor's degree in Computer and Information Sciences from the University of Oregon in 2018. He then worked as a Senior Research Technician in the Dosenbach and Greene Labs at Washington University in St. Louis School of Medicine. At WUSM, Ryland helped develop FIRMM (a software that tracks motion in real-time during functional MRI scans), maintained and improved scripts to analyze resting state functional MRI data, and taught programming skills to other lab members. He is currently completing his Master’s degree in the Cognitive Neuroscience of Language and working as a research assistant at the BCBL.  His main focus is on the proper and efficient use of computing resources in fMRI data analysis. To this end, he works on improving methodologies for MRI data collection, storage, and analysis and on teaching other researchers about these best practices."
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+abstract: "Abstract: In the early 2000s, sharing neuroimaging data was a monumental task that was often not feasible. Each lab had their own way of organizing and naming the multitude of different possible files. The Brain Imaging Data Structure (BIDS) was introduced as an effort to correct this problem. By standardizing the format in which data is stored, it not only makes sharing data simple and easy, but also allows for software to be developed that will work on any data formatted according to BIDS. Thus, it is an important tool for any researcher in a modern world of open science and reproducibility. In this tutorial, Ryland and David will explain the basics of the BIDS format and then go into more in-depth examples of how to move datasets from their raw format into BIDS. David will talk about brain magnetic resonance imaging (MRI) data, whereas Ryland will talk about electroencephalography (EEG) data."
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_posts/2023-09-22-project-3.markdown

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+title: Variability in functional cortical organization
+subtitle: "Bianca Serio - PhD Student @  Max Planck School of Cognition, Max Planck Institute for Human Cognitive and Brain Sciences"
+layout: default
+modal-id: 4
+date: 2024-11-26
+img: 
+thumbnail: 
+alt: image-alt
+project-date: November 2025
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+category: 
+description: "Bianca earned a BSc in Psychology and an MRes in Developmental Neuroscience and Psychopathology from University College London (UK). She conducted research for her Master’s thesis at Yale University (USA), taking a multidimensional approach to understand the emergence of sex differences in internalizing symptoms in adolescence. She is currently a final year PhD student at the Max Planck School of Cognition, based at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig (Germany). Her research focuses on applying computational approaches to investigate principles of functional brain organization, more specifically studying how features of functional connectivity vary within and between individuals, taking evidence from sex differences, deep phenotyping, pubertal development, and psychopathology. She uses multimodal data in her work, derived from human neuroimaging, serum and salivary hormone sampling, clinical assessments, and self-reported questionnaires. Ultimately, Bianca aims for her work to highlight the importance of considering sex as a biological variable in clinical research to improve health outcomes, particularly in the field of women’s health, which has historically been largely neglected."
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+abstract: "The sensorimotor-association (S-A) axis is considered to be a key principle of macroscale cortical organization that differentiates unimodal primary/sensorimotor cortical regions from heteromodal/association regions involved in more complex cognitive functions. Although patterns of functional connectivity along this axis are considered to be broadly stable trait-like features of the human brain, there is still a notable degree of variability, both within and between individuals. In this talk, Bianca will present her research on variability in the S-A axis, taking evidence from sex differences and intra-individual differences, and leveraging human neuroimaging open data that bridges across scales - from the dense sampling of deeply phenotyped single individuals to large population neuroscience study consortia."
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_posts/2023-09-22-project-4.markdown

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+title: TBD
+subtitle: "Eva Méndez - Associate Professor @ Universidad Carlos III de Madrid "
+layout: default
+modal-id: 5
+date: 2024-11-26
+img: 
+thumbnail: 
+alt: image-alt
+project-date: November 2025
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+category: 
+description: "Eva is a professor in the Department of Library and Information Science at Carlos III University of Madrid, where she has also been the Deputy Vice-Chancellor of Scientific Policy and Strategy and Digital Education. She is the director of the OpenScienceLab research group where various meta-research projects for Open Science are developed, including citizen science as a fundamental component of Open Science. Dr. Méndez was the president of the European Commission's Open Science Policy Platform (2018-2020) and is currently a member of the Board of Directors of CoARA (Coalition for Advancing Research Assessment)."
+abstract: TBD
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_posts/2023-09-22-project-5.markdown

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+title: What crosses your mind when you sleep? Cognitive processes and conscious experience in the sleeping brain.
+subtitle: "Nicolas Decat - PhD Student @ Paris Brain Institute "
+layout: default
+modal-id: 2
+date: 2024-11-27
+img: 
+thumbnail: 
+alt: image-alt
+project-date: November 2024
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+category:
+description: "Nicolas’ training focused on cognitive science, completing my Bachelor's and Master's degrees in Lille University (France), the University of Nebraska at Omaha (USA), and the University of Trento (Italy). He specialised in the field of sleep and consciousness through research experiences on the link between mind-wandering and creativity, on the neural correlates of lucid dreaming and on a clustering approach to better characterize sleep (CHUV Lausanne, Switzerland; Monash Biomedical Imaging, Australia; Wisconsin Institute for Sleep and Consciousness, USA). He is now a 2nd-year PhD student at the Paris Brain Institute, supervised by Delphine Oudiette et Thomas Andrillon. Nicolas is interested in what crosses our mind as we fall asleep. he uses high-density EEG to Investigate how the sleep onset period favors creative insight and characterize conscious experiences occurring during this transitory state using machine learning."
+abstract: "As we drift into sleep, our body becomes still, our breathing slows down, and we gradually lose awareness of our surroundings. Though the body appears to go into standby mode, the brain remains active, producing a variety of conscious experiences throughout the night. These experiences range from simple thoughts to intricate and immersive dreams. The nature and purpose of these nocturnal conscious experiences have been a subject of much research. Using high-density electroencephalography (EEG) and serial awakening paradigms, research has attempted to link mental content with specific signatures of brain activity to understand the mechanisms underlying the fluctuations of conscious experience during sleep. Furthermore, incorporating  memory, creativity and perception tasks into these paradigms shed light on the potential roles that dreams play in our waking cognition.  In addition, I will discuss the significance of effective scientific communication in research. Scientific concepts, like consciousness and many others, can be difficult to grasp. Clear communication ensures that findings are understood, replicated, and built upon. It also makes scientific concepts more accessible and engaging, fostering a deeper appreciation for science. Data visualization and storytelling-based talks are crucial tools in bridging the gap between complex research and public understanding, thereby enhancing the overall impact of scientific endeavors."
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